GROMACS version:2018.1
GROMACS modification: No
Hello, I am relatively new to using GROMACS for MD and I have previously used it for membrane systems. Currently I am trying to run protein-ligand complex simulation of 200ns and use frames generated in the last 100ns to estimate mmbpsa…
As for my ligand, I tried to generate parameters with CGenFF but the penalty was very high. Alternatively, I have used SWISSPARAM to generate parameters, and this outputs different extension files of my ligand (.itp; .par; .pdb; .crd …). I have followed the protein-ligand tutorial (changed topol.top file and modified complex gro, made a box, and filled it up with solvent), until I reached adding ions step (gmx grompp -f ions.mdp -c complex_solv.gro -p topol.top -o ions.tpr), I have got numerous warnings and errors saying:
Ignoring obsolete mdp entry ‘title’
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 -1328962596
WARNING 1 [file 63j.prm, line 1]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 2 [file 63j.prm, line 2]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 3 [file 63j.prm, line 3]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 4 [file 63j.prm, line 4]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 5 [file 63j.prm, line 5]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 6 [file 63j.prm, line 7]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
ERROR 1 [file 63j.prm, line 8]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 2 [file 63j.prm, line 9]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 3 [file 63j.prm, line 10]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 4 [file 63j.prm, line 11]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 5 [file 63j.prm, line 12]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 6 [file 63j.prm, line 13]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 7 [file 63j.prm, line 14]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 8 [file 63j.prm, line 15]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 9 [file 63j.prm, line 16]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 10 [file 63j.prm, line 17]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 11 [file 63j.prm, line 18]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 12 [file 63j.prm, line 19]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 13 [file 63j.prm, line 20]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 14 [file 63j.prm, line 21]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 15 [file 63j.prm, line 22]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 16 [file 63j.prm, line 23]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 17 [file 63j.prm, line 24]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 18 [file 63j.prm, line 25]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 19 [file 63j.prm, line 26]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 20 [file 63j.prm, line 27]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
WARNING 7 [file 63j.prm, line 29]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 8 [file 63j.prm, line 30]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 9 [file 63j.prm, line 31]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 10 [file 63j.prm, line 32]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 11 [file 63j.prm, line 33]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 12 [file 63j.prm, line 34]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 13 [file 63j.prm, line 35]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 14 [file 63j.prm, line 36]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 15 [file 63j.prm, line 37]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 16 [file 63j.prm, line 38]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 17 [file 63j.prm, line 39]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 18 [file 63j.prm, line 40]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 19 [file 63j.prm, line 41]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 20 [file 63j.prm, line 42]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 21 [file 63j.prm, line 43]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 22 [file 63j.prm, line 44]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 23 [file 63j.prm, line 45]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 24 [file 63j.prm, line 46]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 25 [file 63j.prm, line 47]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 26 [file 63j.prm, line 48]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 27 [file 63j.prm, line 49]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 28 [file 63j.prm, line 50]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 29 [file 63j.prm, line 51]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 30 [file 63j.prm, line 52]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 31 [file 63j.prm, line 53]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 32 [file 63j.prm, line 54]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 33 [file 63j.prm, line 55]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 34 [file 63j.prm, line 56]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 35 [file 63j.prm, line 57]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 36 [file 63j.prm, line 58]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 37 [file 63j.prm, line 59]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 38 [file 63j.prm, line 60]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 39 [file 63j.prm, line 61]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 40 [file 63j.prm, line 62]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 41 [file 63j.prm, line 63]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 42 [file 63j.prm, line 64]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 43 [file 63j.prm, line 65]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 44 [file 63j.prm, line 66]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 45 [file 63j.prm, line 67]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 46 [file 63j.prm, line 69]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 47 [file 63j.prm, line 70]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 48 [file 63j.prm, line 71]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 49 [file 63j.prm, line 72]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 50 [file 63j.prm, line 73]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 51 [file 63j.prm, line 74]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 52 [file 63j.prm, line 75]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 53 [file 63j.prm, line 76]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 54 [file 63j.prm, line 77]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 55 [file 63j.prm, line 78]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 56 [file 63j.prm, line 79]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 57 [file 63j.prm, line 80]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 58 [file 63j.prm, line 81]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 59 [file 63j.prm, line 82]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 60 [file 63j.prm, line 83]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 61 [file 63j.prm, line 84]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 62 [file 63j.prm, line 85]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 63 [file 63j.prm, line 86]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 64 [file 63j.prm, line 87]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 65 [file 63j.prm, line 88]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 66 [file 63j.prm, line 89]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 67 [file 63j.prm, line 90]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 68 [file 63j.prm, line 91]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 69 [file 63j.prm, line 92]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 70 [file 63j.prm, line 93]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 71 [file 63j.prm, line 94]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 72 [file 63j.prm, line 95]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 73 [file 63j.prm, line 96]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 74 [file 63j.prm, line 97]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 75 [file 63j.prm, line 98]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 76 [file 63j.prm, line 99]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 77 [file 63j.prm, line 100]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 78 [file 63j.prm, line 101]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 79 [file 63j.prm, line 102]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 80 [file 63j.prm, line 103]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 81 [file 63j.prm, line 104]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 82 [file 63j.prm, line 105]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 83 [file 63j.prm, line 106]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 84 [file 63j.prm, line 107]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 85 [file 63j.prm, line 108]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 86 [file 63j.prm, line 109]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 87 [file 63j.prm, line 110]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 88 [file 63j.prm, line 111]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 89 [file 63j.prm, line 112]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 90 [file 63j.prm, line 113]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 91 [file 63j.prm, line 114]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 92 [file 63j.prm, line 115]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 93 [file 63j.prm, line 116]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 94 [file 63j.prm, line 117]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 95 [file 63j.prm, line 118]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 96 [file 63j.prm, line 119]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 97 [file 63j.prm, line 120]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 98 [file 63j.prm, line 121]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 99 [file 63j.prm, line 122]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 100 [file 63j.prm, line 123]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 101 [file 63j.prm, line 124]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 102 [file 63j.prm, line 125]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 103 [file 63j.prm, line 126]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 104 [file 63j.prm, line 127]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 105 [file 63j.prm, line 128]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 106 [file 63j.prm, line 129]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 107 [file 63j.prm, line 130]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 108 [file 63j.prm, line 131]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 109 [file 63j.prm, line 132]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 110 [file 63j.prm, line 133]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 111 [file 63j.prm, line 134]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 112 [file 63j.prm, line 135]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 113 [file 63j.prm, line 136]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 114 [file 63j.prm, line 137]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 115 [file 63j.prm, line 138]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 116 [file 63j.prm, line 139]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 117 [file 63j.prm, line 140]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 118 [file 63j.prm, line 141]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 119 [file 63j.prm, line 142]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 120 [file 63j.prm, line 143]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 121 [file 63j.prm, line 144]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 122 [file 63j.prm, line 145]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 123 [file 63j.prm, line 146]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 124 [file 63j.prm, line 147]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 125 [file 63j.prm, line 148]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 126 [file 63j.prm, line 150]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 127 [file 63j.prm, line 151]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 128 [file 63j.prm, line 152]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 129 [file 63j.prm, line 153]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 130 [file 63j.prm, line 154]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 131 [file 63j.prm, line 155]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 132 [file 63j.prm, line 156]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 133 [file 63j.prm, line 157]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 134 [file 63j.prm, line 158]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 135 [file 63j.prm, line 159]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 136 [file 63j.prm, line 160]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 137 [file 63j.prm, line 161]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 138 [file 63j.prm, line 162]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 139 [file 63j.prm, line 163]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 140 [file 63j.prm, line 164]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 141 [file 63j.prm, line 165]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
WARNING 142 [file 63j.prm, line 166]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
ERROR 21 [file 63j.prm, line 168]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
WARNING 143 [file 63j.prm, line 169]:
Too few parameters on line (source file
/build/gromacs-Fqu8ou/gromacs-2018.1/src/gromacs/gmxpreprocess/toppush.cpp, line 977)
ERROR 22 [file 63j.prm, line 170]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 23 [file 63j.prm, line 171]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 24 [file 63j.prm, line 172]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 25 [file 63j.prm, line 173]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 26 [file 63j.prm, line 174]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 27 [file 63j.prm, line 175]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 28 [file 63j.prm, line 176]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 29 [file 63j.prm, line 177]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 30 [file 63j.prm, line 178]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 31 [file 63j.prm, line 179]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 32 [file 63j.prm, line 180]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 33 [file 63j.prm, line 181]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 34 [file 63j.prm, line 182]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Generated 100032 of the 100128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 65937 of the 100128 1-4 parameter combinations
ERROR 35 [file 63j.itp, line 14]:
Atomtype C5A not found
There was 1 note
There were 143 warnings
Program: gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1390)
Fatal error:
There were 35 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
I assume it is related to the .prm and .itp files generated by swissparam. If that is the problem, does anyone has advice on how to change it and whether there is some other software (supposedly better) for generating more “accurate” ligand parameters?
Many thanks in advance!
Best,
Srdan