Error adding ion

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1

GROMACS version: 5.1.4
GROMACS modification: No
Here post your question

Hello Users, I am running protein-ligand complex simulation using gromacs and i got the following error at the addition of ion step. I think it has to do with ligand topology which i generated using cgenff server. I then generate another one using swissparam and still got the same error. Please does anyone has solution to this?

GROMACS: gmx grompp, VERSION 5.1.4
Executable: /home/apps/gromacs-5.1.4/bin/gmx
Data prefix: /home/apps/gromacs-5.1.4
Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1

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 1934407708

WARNING 1 [file p55_fix.par, line 1]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 2 [file p55_fix.par, line 2]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 3 [file p55_fix.par, line 3]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 4 [file p55_fix.par, line 4]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 5 [file p55_fix.par, line 5]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 6 [file p55_fix.par, line 7]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

ERROR 1 [file p55_fix.par, line 8]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 2 [file p55_fix.par, line 9]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 3 [file p55_fix.par, line 10]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 4 [file p55_fix.par, line 11]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 5 [file p55_fix.par, line 12]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 6 [file p55_fix.par, line 13]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 7 [file p55_fix.par, line 14]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 8 [file p55_fix.par, line 15]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 9 [file p55_fix.par, line 16]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 10 [file p55_fix.par, line 17]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

WARNING 7 [file p55_fix.par, line 19]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 8 [file p55_fix.par, line 20]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 9 [file p55_fix.par, line 21]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 10 [file p55_fix.par, line 22]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 11 [file p55_fix.par, line 23]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 12 [file p55_fix.par, line 24]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 13 [file p55_fix.par, line 25]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 14 [file p55_fix.par, line 26]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 15 [file p55_fix.par, line 27]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 16 [file p55_fix.par, line 28]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 17 [file p55_fix.par, line 29]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 18 [file p55_fix.par, line 30]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 19 [file p55_fix.par, line 31]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 20 [file p55_fix.par, line 32]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 21 [file p55_fix.par, line 33]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 22 [file p55_fix.par, line 35]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 23 [file p55_fix.par, line 36]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 24 [file p55_fix.par, line 37]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 25 [file p55_fix.par, line 38]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 26 [file p55_fix.par, line 39]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 27 [file p55_fix.par, line 40]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 28 [file p55_fix.par, line 41]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 29 [file p55_fix.par, line 42]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 30 [file p55_fix.par, line 43]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 31 [file p55_fix.par, line 44]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 32 [file p55_fix.par, line 45]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 33 [file p55_fix.par, line 46]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 34 [file p55_fix.par, line 47]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 35 [file p55_fix.par, line 48]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 36 [file p55_fix.par, line 49]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 37 [file p55_fix.par, line 50]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 38 [file p55_fix.par, line 51]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 39 [file p55_fix.par, line 52]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 40 [file p55_fix.par, line 53]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 41 [file p55_fix.par, line 54]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 42 [file p55_fix.par, line 55]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 43 [file p55_fix.par, line 56]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 44 [file p55_fix.par, line 57]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 45 [file p55_fix.par, line 58]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 46 [file p55_fix.par, line 59]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 47 [file p55_fix.par, line 60]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 48 [file p55_fix.par, line 61]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 49 [file p55_fix.par, line 63]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 50 [file p55_fix.par, line 64]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 51 [file p55_fix.par, line 65]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 52 [file p55_fix.par, line 66]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 53 [file p55_fix.par, line 67]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 54 [file p55_fix.par, line 68]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

WARNING 55 [file p55_fix.par, line 69]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

ERROR 11 [file p55_fix.par, line 71]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

WARNING 56 [file p55_fix.par, line 72]:
Too few parameters on line (source file
/root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)

ERROR 12 [file p55_fix.par, line 73]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 13 [file p55_fix.par, line 74]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 14 [file p55_fix.par, line 75]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 15 [file p55_fix.par, line 76]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 16 [file p55_fix.par, line 77]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 17 [file p55_fix.par, line 78]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

ERROR 18 [file p55_fix.par, line 79]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations

Program gmx grompp, VERSION 5.1.4
Source code file: /root/_src/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c, line: 755

Fatal error:
Syntax error - File p55_fix.itp, line 7
Last line read:
'[ atomtypes ] ’
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs

2

Please upload your ligand topology and parameter files somewhere. They are apparently syntactically incorrect, and a CHARMM topology should never make use of Buckingham. Nothing produced by the CGenFF server will contain such a functional form. The fatal error suggests you have #include statements that are out of order, which may be an additional problem or the root cause. Without your actual files, it’s hard to tell.

Also, do not get in the habit of using -maxwarn with grompp. It is unwise.

3

Since I cannot upload the file format, I will paste them below.

ligand.prm

[ bondtypes ]
; i j func b0 kb

[ angletypes ]
; i j k func theta0 ktheta ub0 kub
CG321 CG2R53 OG2R50 5 120.000000 383.254400 0.00000000 0.00
CG2R62 CG2R61 CG2RC0 5 120.000000 418.400000 0.00000000 0.00
CG2R53 CG321 NG2R61 5 115.200000 443.504000 0.00000000 0.00
CG2R61 CG321 NG2R61 5 115.200000 443.504000 0.00000000 0.00
CG2R62 NG2R61 CG321 5 117.660000 223.509280 0.00000000 0.00

[ dihedraltypes ]
; i j k l func phi0 kphi mult
NG2R50 CG2R53 CG321 NG2R61 9 180.000000 1.522139 1
NG2R50 CG2R53 CG321 NG2R61 9 0.000000 0.062342 2
NG2R50 CG2R53 CG321 NG2R61 9 180.000000 1.188674 3
NG2R50 CG2R53 CG321 NG2R61 9 0.000000 0.123428 6
OG2R50 CG2R53 CG321 NG2R61 9 0.000000 3.695727 1
OG2R50 CG2R53 CG321 NG2R61 9 0.000000 0.211710 2
OG2R50 CG2R53 CG321 NG2R61 9 180.000000 0.749354 3
OG2R50 CG2R53 CG321 NG2R61 9 180.000000 0.066107 6
OG2R50 CG2R53 CG321 HGA2 9 0.000000 0.794960 3
CG2R61 CG2R53 NG2R50 CG2R53 9 180.000000 16.736000 2
CG2R61 CG2R53 NG2R50 OG2R50 9 180.000000 16.736000 2
CG321 CG2R53 NG2R50 CG2R53 9 180.000000 23.012000 2
CG321 CG2R53 OG2R50 NG2R50 9 180.000000 37.656000 2
CG2R66 CG2R61 CG2R61 CG321 9 180.000000 12.970400 2
CG2RC0 CG2R61 CG2R62 CG2R62 9 180.000000 2.092000 2
CG2RC0 CG2R61 CG2R62 CG2R63 9 180.000000 12.970400 2
CG2RC0 CG2R61 CG2R62 NG2R61 9 180.000000 29.288000 2
CG2R62 CG2R61 CG2RC0 CG2RC0 9 180.000000 12.552000 2
CG2R62 CG2R61 CG2RC0 OG3C51 9 180.000000 8.368000 2
CG2R61 CG2R61 CG321 NG2R61 9 0.000000 0.497896 2
CG2R61 CG2R61 CG321 NG2R61 9 180.000000 0.552288 4
CG2R61 CG2R61 CG321 NG2R61 9 180.000000 0.054392 6
CG2R61 CG2R62 NG2R61 CG321 9 180.000000 46.024000 2
CG2R62 CG2R62 NG2R61 CG321 9 180.000000 46.024000 2
CG2R53 CG321 NG2R61 CG2R63 9 0.000000 2.092000 2
CG2R61 CG321 NG2R61 CG2R62 9 0.000000 7.070960 1
CG2R61 CG321 NG2R61 CG2R63 9 0.000000 2.092000 2
HGA2 CG321 NG2R61 CG2R62 9 0.000000 0.000000 3

[ dihedraltypes ]
; ‘improper’ dihedrals
; i j k l func phi0 kphi

ligand.itp
; Created by cgenff_charmm2gmx.py

[ moleculetype ]
; Name nrexcl
F34 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 F34 rtp F34 q qsum
1 FGR1 1 F34 F1 1 -0.210 18.998 ;
2 CG2R66 1 F34 C1 2 0.137 12.011 ;
3 CG2R61 1 F34 C2 3 -0.103 12.011 ;
4 CG2R61 1 F34 C3 4 -0.058 12.011 ;
5 CG321 1 F34 C4 5 0.050 12.011 ;
6 NG2R61 1 F34 N1 6 -0.573 14.007 ;
7 CG2R63 1 F34 C5 7 0.695 12.011 ;
8 OG2D4 1 F34 O1 8 -0.508 15.999 ;
9 NG2R61 1 F34 N2 9 -0.194 14.007 ;
10 CG321 1 F34 C6 10 0.153 12.011 ;
11 CG2R53 1 F34 C7 11 0.400 12.011 ;
12 NG2R50 1 F34 N3 12 -0.590 14.007 ;
13 CG2R53 1 F34 C8 13 0.584 12.011 ;
14 NG2R50 1 F34 N4 14 -0.444 14.007 ;
15 OG2R50 1 F34 O2 15 -0.184 15.999 ;
16 CG2R61 1 F34 C9 16 0.077 12.011 ;
17 CG2R61 1 F34 C10 17 -0.110 12.011 ;
18 CG2R61 1 F34 C11 18 -0.110 12.011 ;
19 CG2R61 1 F34 C12 19 -0.115 12.011 ;
20 CG2R61 1 F34 C13 20 -0.110 12.011 ;
21 CG2R61 1 F34 C14 21 -0.110 12.011 ;
22 CG2R63 1 F34 C15 22 0.482 12.011 ;
23 OG2D4 1 F34 O3 23 -0.473 15.999 ;
24 CG2R62 1 F34 C16 24 -0.140 12.011 ;
25 CG2R61 1 F34 C17 25 -0.375 12.011 ;
26 CG2RC0 1 F34 C18 26 0.074 12.011 ;
27 CG2RC0 1 F34 C19 27 0.080 12.011 ;
28 OG3C51 1 F34 O4 28 -0.272 15.999 ;
29 CG3C52 1 F34 C20 29 0.416 12.011 ;
30 OG3C51 1 F34 O5 30 -0.272 15.999 ;
31 CG2R61 1 F34 C21 31 -0.356 12.011 ;
32 CG2R62 1 F34 C22 32 0.254 12.011 ;
33 CG2R61 1 F34 C23 33 -0.107 12.011 ;
34 CG2R61 1 F34 C24 34 -0.166 12.011 ;
35 CG2R61 1 F34 C25 35 -0.089 12.011 ;
36 HGR62 1 F34 H1 36 0.181 1.008 ;
37 HGA2 1 F34 H2 37 0.090 1.008 ;
38 HGA2 1 F34 H3 38 0.090 1.008 ;
39 HGA2 1 F34 H4 39 0.090 1.008 ;
40 HGA2 1 F34 H5 40 0.090 1.008 ;
41 HGR61 1 F34 H6 41 0.115 1.008 ;
42 HGR61 1 F34 H7 42 0.115 1.008 ;
43 HGR61 1 F34 H8 43 0.115 1.008 ;
44 HGR61 1 F34 H9 44 0.115 1.008 ;
45 HGR61 1 F34 H10 45 0.115 1.008 ;
46 HGR61 1 F34 H11 46 0.280 1.008 ;
47 HGA2 1 F34 H12 47 0.090 1.008 ;
48 HGA2 1 F34 H13 48 0.090 1.008 ;
49 HGR61 1 F34 H14 49 0.280 1.008 ;
50 HGR61 1 F34 H15 50 0.115 1.008 ;
51 HGR61 1 F34 H16 51 0.115 1.008 ;
52 HGR62 1 F34 H17 52 0.181 1.008 ;

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
2 3 1
2 35 1
3 4 1
3 36 1
4 33 1
4 5 1
5 37 1
5 6 1
5 38 1
6 7 1
6 32 1
7 9 1
7 8 1
9 10 1
9 22 1
10 11 1
10 39 1
10 40 1
11 12 1
11 15 1
12 13 1
13 14 1
13 16 1
14 15 1
16 17 1
16 21 1
17 41 1
17 18 1
18 42 1
18 19 1
19 43 1
19 20 1
20 44 1
20 21 1
21 45 1
22 23 1
22 24 1
24 25 1
24 32 1
25 26 1
25 46 1
26 27 1
26 30 1
27 28 1
27 31 1
28 29 1
29 30 1
29 47 1
29 48 1
31 49 1
31 32 1
33 34 1
33 50 1
34 35 1
34 51 1
35 52 1

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 36 1
1 4 1
1 52 1
1 34 1
2 33 1
2 51 1
2 5 1
3 34 1
3 37 1
3 38 1
3 50 1
3 52 1
3 6 1
4 35 1
4 51 1
4 7 1
4 32 1
5 36 1
5 34 1
5 8 1
5 9 1
5 50 1
5 24 1
5 31 1
6 33 1
6 10 1
6 49 1
6 22 1
6 25 1
6 27 1
7 37 1
7 38 1
7 39 1
7 40 1
7 11 1
7 23 1
7 24 1
7 31 1
8 10 1
8 22 1
8 32 1
9 25 1
9 12 1
9 15 1
9 32 1
10 13 1
10 14 1
10 23 1
10 24 1
11 22 1
11 16 1
12 17 1
12 21 1
12 39 1
12 40 1
13 41 1
13 20 1
13 45 1
13 18 1
14 17 1
14 21 1
15 16 1
15 39 1
15 40 1
16 42 1
16 44 1
16 19 1
17 20 1
17 43 1
17 45 1
18 44 1
18 21 1
19 41 1
19 45 1
20 42 1
21 41 1
21 43 1
22 39 1
22 40 1
22 46 1
22 26 1
22 31 1
23 25 1
23 32 1
24 49 1
24 27 1
24 30 1
25 28 1
25 29 1
25 31 1
26 49 1
26 48 1
26 47 1
26 32 1
27 48 1
27 46 1
27 47 1
28 49 1
28 32 1
29 31 1
30 46 1
30 31 1
32 37 1
32 38 1
32 46 1
33 36 1
33 37 1
33 52 1
33 38 1
35 36 1
35 50 1
41 42 1
42 43 1
43 44 1
44 45 1
50 51 1
51 52 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 5
1 2 35 5
3 2 35 5
2 3 4 5
2 3 36 5
4 3 36 5
33 4 3 5
33 4 5 5
3 4 5 5
4 5 37 5
4 5 6 5
4 5 38 5
37 5 6 5
37 5 38 5
6 5 38 5
5 6 7 5
5 6 32 5
7 6 32 5
9 7 6 5
9 7 8 5
6 7 8 5
10 9 22 5
10 9 7 5
22 9 7 5
9 10 11 5
9 10 39 5
9 10 40 5
11 10 39 5
11 10 40 5
39 10 40 5
10 11 12 5
10 11 15 5
12 11 15 5
11 12 13 5
12 13 14 5
12 13 16 5
14 13 16 5
13 14 15 5
11 15 14 5
17 16 21 5
17 16 13 5
21 16 13 5
41 17 18 5
41 17 16 5
18 17 16 5
17 18 42 5
17 18 19 5
42 18 19 5
18 19 43 5
18 19 20 5
43 19 20 5
19 20 44 5
19 20 21 5
44 20 21 5
20 21 45 5
20 21 16 5
45 21 16 5
9 22 23 5
9 22 24 5
23 22 24 5
25 24 22 5
25 24 32 5
22 24 32 5
26 25 46 5
26 25 24 5
46 25 24 5
25 26 27 5
25 26 30 5
27 26 30 5
26 27 28 5
26 27 31 5
28 27 31 5
27 28 29 5
28 29 30 5
28 29 47 5
28 29 48 5
30 29 47 5
30 29 48 5
47 29 48 5
26 30 29 5
49 31 27 5
49 31 32 5
27 31 32 5
6 32 31 5
6 32 24 5
31 32 24 5
34 33 4 5
34 33 50 5
4 33 50 5
33 34 35 5
33 34 51 5
35 34 51 5
2 35 52 5
2 35 34 5
52 35 34 5

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 2 3 4 9
1 2 3 36 9
35 2 3 4 9
35 2 3 36 9
1 2 35 52 9
1 2 35 34 9
3 2 35 52 9
3 2 35 34 9
2 3 4 33 9
2 3 4 5 9
36 3 4 33 9
36 3 4 5 9
3 4 33 34 9
3 4 33 50 9
5 4 33 34 9
5 4 33 50 9
33 4 5 37 9
33 4 5 6 9
33 4 5 38 9
3 4 5 37 9
3 4 5 6 9
3 4 5 38 9
4 5 6 7 9
4 5 6 32 9
37 5 6 7 9
37 5 6 32 9
38 5 6 7 9
38 5 6 32 9
5 6 7 9 9
5 6 7 8 9
32 6 7 9 9
32 6 7 8 9
5 6 32 31 9
5 6 32 24 9
7 6 32 31 9
7 6 32 24 9
6 7 9 10 9
6 7 9 22 9
8 7 9 10 9
8 7 9 22 9
22 9 10 11 9
22 9 10 39 9
22 9 10 40 9
7 9 10 11 9
7 9 10 39 9
7 9 10 40 9
10 9 22 23 9
10 9 22 24 9
7 9 22 23 9
7 9 22 24 9
9 10 11 12 9
9 10 11 15 9
39 10 11 12 9
39 10 11 15 9
40 10 11 12 9
40 10 11 15 9
10 11 12 13 9
15 11 12 13 9
10 11 15 14 9
12 11 15 14 9
11 12 13 14 9
11 12 13 16 9
12 13 14 15 9
16 13 14 15 9
12 13 16 17 9
12 13 16 21 9
14 13 16 17 9
14 13 16 21 9
13 14 15 11 9
21 16 17 41 9
21 16 17 18 9
13 16 17 41 9
13 16 17 18 9
17 16 21 20 9
17 16 21 45 9
13 16 21 20 9
13 16 21 45 9
41 17 18 42 9
41 17 18 19 9
16 17 18 42 9
16 17 18 19 9
17 18 19 43 9
17 18 19 20 9
42 18 19 43 9
42 18 19 20 9
18 19 20 44 9
18 19 20 21 9
43 19 20 44 9
43 19 20 21 9
19 20 21 45 9
19 20 21 16 9
44 20 21 45 9
44 20 21 16 9
9 22 24 25 9
9 22 24 32 9
23 22 24 25 9
23 22 24 32 9
22 24 25 26 9
22 24 25 46 9
32 24 25 26 9
32 24 25 46 9
25 24 32 6 9
25 24 32 31 9
22 24 32 6 9
22 24 32 31 9
46 25 26 27 9
46 25 26 30 9
24 25 26 27 9
24 25 26 30 9
25 26 27 28 9
25 26 27 31 9
30 26 27 28 9
30 26 27 31 9
25 26 30 29 9
27 26 30 29 9
26 27 28 29 9
31 27 28 29 9
26 27 31 49 9
26 27 31 32 9
28 27 31 49 9
28 27 31 32 9
27 28 29 30 9
27 28 29 47 9
27 28 29 48 9
28 29 30 26 9
47 29 30 26 9
48 29 30 26 9
49 31 32 6 9
49 31 32 24 9
27 31 32 6 9
27 31 32 24 9
4 33 34 35 9
4 33 34 51 9
50 33 34 35 9
50 33 34 51 9
33 34 35 2 9
33 34 35 52 9
51 34 35 2 9
51 34 35 52 9

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
7 6 9 8 2
22 24 9 23 2

ligand.top
f34.top (454 Bytes)

ligand.gro
Gnomes, ROck Monsters And Chili Sauce
52
1F34 F1 1 -0.204 -0.935 -0.291
1F34 C1 2 -0.218 -0.924 -0.161
1F34 C2 3 -0.128 -0.845 -0.086
1F34 C3 4 -0.142 -0.833 0.054
1F34 C4 5 -0.047 -0.751 0.135
1F34 N1 6 -0.112 -0.646 0.214
1F34 C5 7 -0.157 -0.534 0.147
1F34 O1 8 -0.154 -0.533 0.021
1F34 N2 9 -0.206 -0.423 0.212
1F34 C6 10 -0.256 -0.307 0.137
1F34 C7 11 -0.404 -0.301 0.144
1F34 N3 12 -0.490 -0.344 0.050
1F34 C8 13 -0.612 -0.331 0.105
1F34 N4 14 -0.599 -0.277 0.227
1F34 O2 15 -0.473 -0.258 0.251
1F34 C9 16 -0.736 -0.371 0.049
1F34 C10 17 -0.843 -0.405 0.134
1F34 C11 18 -0.967 -0.444 0.082
1F34 C12 19 -0.987 -0.449 -0.057
1F34 C13 20 -0.881 -0.415 -0.144
1F34 C14 21 -0.756 -0.377 -0.091
1F34 C15 22 -0.209 -0.423 0.349
1F34 O3 23 -0.244 -0.320 0.411
1F34 C16 24 -0.175 -0.538 0.423
1F34 C17 25 -0.189 -0.542 0.565
1F34 C18 26 -0.161 -0.660 0.634
1F34 C19 27 -0.119 -0.773 0.566
1F34 O4 28 -0.098 -0.877 0.649
1F34 C20 29 -0.113 -0.815 0.778
1F34 O5 30 -0.169 -0.682 0.767
1F34 C21 31 -0.103 -0.771 0.427
1F34 C22 32 -0.128 -0.653 0.351
1F34 C23 33 -0.249 -0.901 0.117
1F34 C24 34 -0.339 -0.980 0.042
1F34 C25 35 -0.324 -0.991 -0.097
1F34 H1 36 -0.047 -0.794 -0.138
1F34 H2 37 -0.002 -0.818 0.207
1F34 H3 38 0.016 -0.698 0.063
1F34 H4 39 -0.220 -0.218 0.189
1F34 H5 40 -0.230 -0.323 0.032
1F34 H6 41 -0.830 -0.401 0.243
1F34 H7 42 -1.049 -0.472 0.149
1F34 H8 43 -1.083 -0.478 -0.098
1F34 H9 44 -0.896 -0.419 -0.251
1F34 H10 45 -0.674 -0.353 -0.159
1F34 H11 46 -0.221 -0.454 0.620
1F34 H12 47 -0.187 -0.875 0.832
1F34 H13 48 -0.013 -0.803 0.819
1F34 H14 49 -0.070 -0.863 0.378
1F34 H15 50 -0.262 -0.893 0.225
1F34 H16 51 -0.420 -1.033 0.093
1F34 H17 52 -0.394 -1.051 -0.155
0.00000 0.00000 0.00000

These are the topology files I generated using cgenff server. The error i received with these files is “No default Proper Dih. types” . However, the error i posted above was the one i got from the topology generated from swissparam.

4

The topology from the CGenFF server should work fine. I can’t speak to anything that SwissParam produces, but I’ve seen a few users report issues with something related to a Buckingham potential, so I suspect their topologies may be incorrectly formatted or there are other implementation details that are not being properly observed when using their topologies.

5

Thank you very much. I will generate the topology again and rerun the job.