Errors adding ions in gmx

User discussions
1

GROMACS version:5.1.4
GROMACS modification: Yes/No
I get following long list of errors while adding ions
GROMACS: gmx grompp, VERSION 5.1.4
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry ‘title’

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#

NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Setting the LD random seed to 4033869107

WARNING 1 [file lig.prm, line 1]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 2 [file lig.prm, line 2]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 3 [file lig.prm, line 3]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 4 [file lig.prm, line 5]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

ERROR 1 [file lig.prm, line 6]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

WARNING 5 [file lig.prm, line 7]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 6 [file lig.prm, line 9]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

ERROR 2 [file lig.prm, line 10]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 3 [file lig.prm, line 11]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 4 [file lig.prm, line 12]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 5 [file lig.prm, line 13]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 6 [file lig.prm, line 14]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 7 [file lig.prm, line 15]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 8 [file lig.prm, line 16]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 9 [file lig.prm, line 17]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 10 [file lig.prm, line 18]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 11 [file lig.prm, line 19]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 12 [file lig.prm, line 20]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 13 [file lig.prm, line 21]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 14 [file lig.prm, line 22]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 15 [file lig.prm, line 23]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 16 [file lig.prm, line 24]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 17 [file lig.prm, line 25]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 18 [file lig.prm, line 26]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 19 [file lig.prm, line 27]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 20 [file lig.prm, line 28]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 21 [file lig.prm, line 29]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

WARNING 7 [file lig.prm, line 31]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 8 [file lig.prm, line 32]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 9 [file lig.prm, line 33]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 10 [file lig.prm, line 34]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 11 [file lig.prm, line 35]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 12 [file lig.prm, line 36]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 13 [file lig.prm, line 37]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 14 [file lig.prm, line 38]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 15 [file lig.prm, line 39]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 16 [file lig.prm, line 40]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 17 [file lig.prm, line 41]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 18 [file lig.prm, line 42]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 19 [file lig.prm, line 43]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 20 [file lig.prm, line 44]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 21 [file lig.prm, line 45]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 22 [file lig.prm, line 46]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 23 [file lig.prm, line 47]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 24 [file lig.prm, line 48]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 25 [file lig.prm, line 49]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 26 [file lig.prm, line 50]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 27 [file lig.prm, line 51]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 28 [file lig.prm, line 52]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 29 [file lig.prm, line 53]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 30 [file lig.prm, line 54]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 31 [file lig.prm, line 55]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 32 [file lig.prm, line 56]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 33 [file lig.prm, line 57]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 34 [file lig.prm, line 58]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 35 [file lig.prm, line 59]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 36 [file lig.prm, line 60]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 37 [file lig.prm, line 61]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 38 [file lig.prm, line 62]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 39 [file lig.prm, line 63]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 40 [file lig.prm, line 64]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 41 [file lig.prm, line 65]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 42 [file lig.prm, line 66]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 43 [file lig.prm, line 67]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 44 [file lig.prm, line 68]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 45 [file lig.prm, line 69]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 46 [file lig.prm, line 71]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 47 [file lig.prm, line 72]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 48 [file lig.prm, line 73]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 49 [file lig.prm, line 74]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 50 [file lig.prm, line 75]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 51 [file lig.prm, line 76]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 52 [file lig.prm, line 77]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 53 [file lig.prm, line 78]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 54 [file lig.prm, line 79]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 55 [file lig.prm, line 80]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 56 [file lig.prm, line 81]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 57 [file lig.prm, line 82]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 58 [file lig.prm, line 83]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 59 [file lig.prm, line 84]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 60 [file lig.prm, line 85]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 61 [file lig.prm, line 86]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 62 [file lig.prm, line 87]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 63 [file lig.prm, line 88]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 64 [file lig.prm, line 89]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 65 [file lig.prm, line 90]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 66 [file lig.prm, line 91]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 67 [file lig.prm, line 92]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 68 [file lig.prm, line 93]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 69 [file lig.prm, line 94]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 70 [file lig.prm, line 95]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 71 [file lig.prm, line 96]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 72 [file lig.prm, line 97]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 73 [file lig.prm, line 98]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 74 [file lig.prm, line 99]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 75 [file lig.prm, line 100]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 76 [file lig.prm, line 101]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 77 [file lig.prm, line 102]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 78 [file lig.prm, line 103]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 79 [file lig.prm, line 104]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 80 [file lig.prm, line 105]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 81 [file lig.prm, line 106]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 82 [file lig.prm, line 107]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 83 [file lig.prm, line 108]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 84 [file lig.prm, line 109]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 85 [file lig.prm, line 110]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 86 [file lig.prm, line 111]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 87 [file lig.prm, line 112]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 88 [file lig.prm, line 113]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 89 [file lig.prm, line 114]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 90 [file lig.prm, line 115]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 91 [file lig.prm, line 116]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 92 [file lig.prm, line 117]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 93 [file lig.prm, line 118]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 94 [file lig.prm, line 119]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 95 [file lig.prm, line 120]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 96 [file lig.prm, line 121]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 97 [file lig.prm, line 122]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 98 [file lig.prm, line 123]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 99 [file lig.prm, line 124]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 100 [file lig.prm, line 125]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 101 [file lig.prm, line 126]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 102 [file lig.prm, line 127]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 103 [file lig.prm, line 128]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 104 [file lig.prm, line 129]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 105 [file lig.prm, line 130]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 106 [file lig.prm, line 131]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 107 [file lig.prm, line 132]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 108 [file lig.prm, line 133]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 109 [file lig.prm, line 134]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 110 [file lig.prm, line 135]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 111 [file lig.prm, line 136]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 112 [file lig.prm, line 137]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 113 [file lig.prm, line 138]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 114 [file lig.prm, line 139]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 115 [file lig.prm, line 140]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 116 [file lig.prm, line 141]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 117 [file lig.prm, line 142]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 118 [file lig.prm, line 143]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 119 [file lig.prm, line 144]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 120 [file lig.prm, line 145]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 121 [file lig.prm, line 147]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 122 [file lig.prm, line 148]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 123 [file lig.prm, line 149]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 124 [file lig.prm, line 151]:
Too few parameters on line (source file
/home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

Generated 100474 of the 100576 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 66298 of the 100576 1-4 parameter combinations

ERROR 22 [file LIG.itp, line 80]:
No default Bond types

ERROR 23 [file LIG.itp, line 92]:
No default Bond types

ERROR 24 [file LIG.itp, line 227]:
No default U-B types

ERROR 25 [file LIG.itp, line 228]:
No default U-B types

ERROR 26 [file LIG.itp, line 229]:
No default U-B types

ERROR 27 [file LIG.itp, line 231]:
No default U-B types

ERROR 28 [file LIG.itp, line 232]:
No default U-B types

ERROR 29 [file LIG.itp, line 234]:
No default U-B types

ERROR 30 [file LIG.itp, line 239]:
No default U-B types

ERROR 31 [file LIG.itp, line 245]:
No default U-B types

ERROR 32 [file LIG.itp, line 264]:
No default U-B types

ERROR 33 [file LIG.itp, line 265]:
No default U-B types

ERROR 34 [file LIG.itp, line 267]:
No default U-B types

ERROR 35 [file LIG.itp, line 268]:
No default U-B types

ERROR 36 [file LIG.itp, line 269]:
No default U-B types

ERROR 37 [file LIG.itp, line 270]:
No default U-B types
ERROR 38 [file LIG.itp, line 272]:
No default U-B types
ERROR 39 [file LIG.itp, line 297]:
No default Proper Dih. types
ERROR 40 [file LIG.itp, line 298]:
No default Proper Dih. types

ERROR 41 [file LIG.itp, line 299]:
No default Proper Dih. types
ERROR 42 [file LIG.itp, line 300]:
No default Proper Dih. types

ERROR 43 [file LIG.itp, line 301]:
No default Proper Dih. types
ERROR 44 [file LIG.itp, line 302]:
No default Proper Dih. types

ERROR 45 [file LIG.itp, line 303]:
No default Proper Dih. types

ERROR 46 [file LIG.itp, line 306]:
No default Proper Dih. types

ERROR 47 [file LIG.itp, line 307]:
No default Proper Dih. types

ERROR 48 [file LIG.itp, line 308]:
No default Proper Dih. types

ERROR 49 [file LIG.itp, line 309]:
No default Proper Dih. types

ERROR 50 [file LIG.itp, line 310]:
No default Proper Dih. types

ERROR 51 [file LIG.itp, line 311]:
No default Proper Dih. types

ERROR 52 [file LIG.itp, line 314]:
No default Proper Dih. types

ERROR 53 [file LIG.itp, line 315]:
No default Proper Dih. types

ERROR 54 [file LIG.itp, line 316]:
No default Proper Dih. types

ERROR 55 [file LIG.itp, line 317]:
No default Proper Dih. types

  1. List item

ERROR 56 [file LIG.itp, line 319]:
No default Proper Dih. types
ERROR 57 [file LIG.itp, line 320]:
No default Proper Dih. types

ERROR 58 [file LIG.itp, line 327]:
No default Proper Dih. types

ERROR 59 [file LIG.itp, line 328]:
No default Proper Dih. types

ERROR 60 [file LIG.itp, line 329]:
No default Proper Dih. types

ERROR 61 [file LIG.itp, line 333]:
No default Proper Dih. types

ERROR 62 [file LIG.itp, line 334]:
No default Proper Dih. types

ERROR 63 [file LIG.itp, line 335]:
No default Proper Dih. types

ERROR 64 [file LIG.itp, line 336]:
No default Proper Dih. types

ERROR 65 [file LIG.itp, line 337]:
No default Proper Dih. types

ERROR 66 [file LIG.itp, line 338]:
No default Proper Dih. types

ERROR 67 [file LIG.itp, line 339]:
No default Proper Dih. types

ERROR 68 [file LIG.itp, line 357]:
No default Proper Dih. types

ERROR 69 [file LIG.itp, line 366]:
No default Proper Dih. types

ERROR 70 [file LIG.itp, line 367]:
No default Proper Dih. types

ERROR 71 [file LIG.itp, line 368]:
No default Proper Dih. types

ERROR 72 [file LIG.itp, line 369]:
No default Proper Dih. types

ERROR 73 [file LIG.itp, line 370]:
No default Proper Dih. types

ERROR 74 [file LIG.itp, line 372]:
No default Proper Dih. types

ERROR 75 [file LIG.itp, line 373]:
No default Proper Dih. types

ERROR 76 [file LIG.itp, line 374]:
No default Proper Dih. types

ERROR 77 [file LIG.itp, line 375]:
No default Proper Dih. types

ERROR 78 [file LIG.itp, line 376]:
No default Proper Dih. types

ERROR 79 [file LIG.itp, line 377]:
No default Proper Dih. types

ERROR 80 [file LIG.itp, line 379]:
No default Proper Dih. types

ERROR 81 [file LIG.itp, line 380]:
No default Proper Dih. types

ERROR 82 [file LIG.itp, line 381]:
No default Proper Dih. types

ERROR 83 [file LIG.itp, line 413]:
No default Improper Dih. types

ERROR 84 [file LIG.itp, line 414]:
No default Improper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘LIG’
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 186407]:
System has non-zero total charge: -6.999988
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.

Removing all charge groups because cutoff-scheme=Verlet

There were 2 notes

There were 124 warnings

Program gmx grompp, VERSION 5.1.4
Source code file: /home/urvashi/Documents/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line: 1738

Fatal error:
There were 84 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

2

It appears your ligand parameters are both syntactically incorrect as well as incompatible with the force field’s functional form. What are you trying to do? How did you create your topology?

3

I followed gromacs tutorial to generate the topology of protein and ligand (later using cgenff server). Then had manually input ligand parameter into protein topology to build the complex and followed solvation and ion adding steps however I am stuck.

4

The CGenFF server should not give you anything related to a Buckingham potential (which is not compatible with CHARMM) and should not have all those syntax errors. You’ll need to share the relevant topology file(s) and tell us what modifications you’ve made to the ligand topology. The topology looks to be basically totally broken.

5

I uploaded sdf file of ligand into cgenff to generate the topology and output mol files which I then processed in the command line option to use chamm 36 forcefield for ligand topology and then combined the two files as per gromacs tutorial (http://www.mdtutorials.com/gmx/complex/02_topology.html)

6

as needed all the topology files and gro files for complex are enclose in dropbox link

7

Dropbox says your files were deleted.

8

sorry here is the drop box link to look into gromacs input generated using CharmmGUI.


The minimization is stuck at md run minimization steps and returns following error.
error at the minimization step:
  • first, a warning from the software at the beginning :
    "WARNING: Listed nonbonded interaction between particles 31319 and 31334
    at distance 2.863 which is larger than the table limit 2.260 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions."

  • then the program crashes after 17 steps of minimization:
    “step 17: One or more water molecules can not be settled.
    Check for bad contacts and/or reduce the timestep if appropriate.
    16736 16735 40.5 0.0997 0.0997 0.0997”

and system/run is hanged beyond this.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason."

Please advice

many thanks in advance,
Urvashi Sharma

9

OK, so the question is no longer related to Buckingham potentials and is now just about the system crashing? Is that correct? The files provided are standard CHARMM-GUI output so there’s nothing I can see about Buckingham.

If minimization is failing, then try a smaller initial emstep or, as the README says, try minimizing in double precision.

10

Thank you for your input.

Yes, the previous question of wrong ligand topology could be solved after several trials.
I didn’t get your point for initial emstep (before equilibration?)
or
as the README says, try minimizing in double precision (how should I do this?), I am new Gromcas user.

11

You said the system is failing in minimization, so the proposed solution is for minimization. emstep is the maximum step size along the gradient. A smaller size can be helpful in relaxing difficult systems.

Recompile GROMACS in double precision. See the manual for instructions.

12

Dear jalemkul,

Could you assist me in understanding the use case for double precision? Is double precision typically employed when single precision encounters limitations?

I am currently conducting simulations on a membrane protein with lipid bilayers. The minimization process successfully converged without resorting to double precision. Are there any specific advantages to performing minimization in double precision, especially when the single precision approach has already achieved convergence?

Thanks

13

Sometimes, but in my experience it doesn’t usually help. Double precision is useful for certain applications, like free energy calculations, normal mode analysis, etc. But if a system doesn’t want to minimize, there’s usually a reason for more fundamental than some limitation in precision.