Topology file for cisplatin

User discussions
1

Dear GROMACS users,

I have a topology file of the cisplatin molecule that I used in my molecular dynamics simulations in the software Amber 16. By using an application available in Amber, I converted the topology file (.prmtop) of this molecule for the topology file (.top) that is compatible with Gromacs, since I am going to use this molecular dynamics package. The topology file for cisplatin inside a water box is:

;
; File cis_gromacs.top was generated
; By user: eduardo (1001)
; On host: inspiron5480
; At date: Tue. June 2 23:35:50 2020
;
; This is a standalone topology file
;
; Created by:
; ParmEd: amber2gromacs.py, VERSION 3.2.0
; Executable: amber2gromacs.py
; Library dir: /usr/share/gromacs/top
; Command line:
; amber2gromacs.py
;

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.83333333

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
Pt 78 195.078000 0.00000000 A 0.45596196 29.32984
c5 17 35.453000 0.00000000 A 0.34709414 1.10876
c6 17 35.453000 0.00000000 A 0.34709414 1.10876
n4 7 14.007000 0.00000000 A 0.32499985 0.71128
hn 1 1.008000 0.00000000 A 0.10690785 0.0656888
n5 7 14.007000 0.00000000 A 0.32499985 0.71128
OW 8 16.000000 0.00000000 A 0.31507524 0.635968
HW 1 1.008000 0.00000000 A 0 0

[ moleculetype ]
; Name nrexcl
MOL 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 MOL rtp MOL q -0.0
1 Pt 1 MOL Pt1 1 0.45754000 195.078000 ; qtot 0.457540
2 c5 1 MOL Cl2 2 -0.61594400 35.453000 ; qtot -0.158404
3 c6 1 MOL Cl3 3 -0.61595300 35.453000 ; qtot -0.774357
4 n4 1 MOL N4 4 -0.55089000 14.007000 ; qtot -1.325247
5 hn 1 MOL H5 5 0.31511500 1.008000 ; qtot -1.010132
6 hn 1 MOL H6 6 0.31793100 1.008000 ; qtot -0.692201
7 n5 1 MOL N7 7 -0.55124100 14.007000 ; qtot -1.243442
8 hn 1 MOL H8 8 0.31523700 1.008000 ; qtot -0.928205
9 hn 1 MOL H9 9 0.31797300 1.008000 ; qtot -0.610232
10 hn 1 MOL H10 10 0.30516900 1.008000 ; qtot -0.305063
11 hn 1 MOL H11 11 0.30506300 1.008000 ; qtot -0.000000

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 0.23900 89495.760000
1 3 1 0.23900 89489.065600
1 4 1 0.20570 99881.284800
1 7 1 0.20570 99883.795200
4 5 1 0.10330 308779.200000
4 6 1 0.10330 308779.200000
4 11 1 0.10330 308779.200000
7 8 1 0.10330 308779.200000
7 9 1 0.10330 308779.200000
7 10 1 0.10330 308779.200000

[ pairs ]
; ai aj funct c0 c1 c2 c3
2 5 1
2 6 1
2 11 1
2 8 1
2 9 1
2 10 1
3 5 1
3 6 1
3 11 1
3 8 1
3 9 1
3 10 1
4 8 1
4 9 1
4 10 1
7 5 1
7 6 1
7 11 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1 94.6200408 776.039952
2 1 4 1 178.1800761 945.835040
2 1 7 1 87.1900375 884.522704
3 1 4 1 87.1900375 884.598016
3 1 7 1 178.1800761 938.571616
4 1 7 1 91.0000390 1022.251616
1 4 5 1 111.6500481 461.696032
1 4 6 1 111.6500481 461.696032
1 4 11 1 111.6500481 461.696032
1 7 8 1 111.6500481 461.696032
1 7 9 1 111.6500481 461.696032
1 7 10 1 111.6500481 461.696032
5 4 6 1 108.1100462 339.071360
5 4 11 1 108.1100462 339.071360
6 4 11 1 108.1100462 339.071360
8 7 9 1 108.1100462 339.071360
8 7 10 1 108.1100462 339.071360
9 7 10 1 108.1100462 339.071360

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 4 5 1 0.0000000 0.0000000 0
2 1 4 6 1 0.0000000 0.0000000 0
2 1 4 11 1 0.0000000 0.0000000 0
2 1 7 8 1 0.0000000 0.0000000 0
2 1 7 9 1 0.0000000 0.0000000 0
2 1 7 10 1 0.0000000 0.0000000 0
3 1 4 5 1 0.0000000 0.0000000 0
3 1 4 6 1 0.0000000 0.0000000 0
3 1 4 11 1 0.0000000 0.0000000 0
3 1 7 8 1 0.0000000 0.0000000 0
3 1 7 9 1 0.0000000 0.0000000 0
3 1 7 10 1 0.0000000 0.0000000 0
4 1 7 8 1 0.0000000 0.0000000 0
4 1 7 9 1 0.0000000 0.0000000 0
4 1 7 10 1 0.0000000 0.0000000 0
7 1 4 5 1 0.0000000 0.0000000 0
7 1 4 6 1 0.0000000 0.0000000 0
7 1 4 11 1 0.0000000 0.0000000 0

[ moleculetype ]
; Name nrexcl
WAT 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 WAT rtp WAT q 0.0
1 OW 1 WAT O 1 -0.83400000 16.000000 ; qtot -0.834000
2 HW 1 WAT H1 2 0.41700000 1.008000 ; qtot -0.417000
3 HW 1 WAT H2 3 0.41700000 1.008000 ; qtot 0.000000

#ifdef FLEXIBLE

[ bonds ]
; ai aj funct c0 c1 c2 c3
2 1 1 0.09572 462750.400000
3 1 1 0.09572 462750.400000
3 2 1 0.15136 462750.400000

#else

[ settles ]
; i funct doh dhh
1 1 0.09572000 0.15136000

#endif

[ exclusions ]
1 2 3
2 1 3
3 1 2

[ system ]
; Name
Generic title

[ molecules ]
; Compound #mols
MOL 1
WAT 1064

However, when I try to submit this file with the .gro file, a fatal error message appears during the equilibration step. I use these lines:

1.Minimization:
gmx grompp -f minim.mdp -c cis_gromacs.gro -p cis_gromacs.top -o em.tpr

gmx mdrun -v -deffnm em

  1. Equilibration:

gmx grompp -f nvt.mdp -c em.gro -r em.gro -p cis_gromacs.top -o nvt.tpr

The error is:

eduardo@inspiron5480:~/Documents/2019_1/TABC/Gromacs_cddp$ gmx grompp -f nvt.mdp -c em.gro -r em.gro -p cis_gromacs.top -o nvt.tpr
:-) GROMACS - gmx grompp, 2018.1 (-:

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Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl
Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola
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Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen
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and the project leaders:
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GROMACS: gmx grompp, version 2018.1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/eduardo/Documents/2019_1/TABC/Gromacs_cddp
Command line:
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p cis_gromacs.top -o nvt.tpr

Ignoring obsolete mdp entry ‘title’
Setting the LD random seed to -1466647373
Generated 36 of the 36 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 36 of the 36 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘MOL’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘WAT’
turning H bonds into constraints…
Setting gen_seed to 180662076
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 1 Other residues
There are: 1064 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…

Program: gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2683)

Fatal error:
Group Non-Protein referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the ‘-n’ option
of grompp.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I would like to ask if anyone could help me with this error.

Sincerely,

Eduardo.

2

Be careful about reusing tutorial or stock .mdp files; they’re generally designed for biomolecular systems. You have a small molecule in water. Your tc-grps should simply be set for System. Since you don’t have any protein in your system, there’s not going to be a Non-Protein group generated, so you can’t specify that in your input as a valid group.

1 Like
3

Dear jalemkul,

Thank you so much for your help! Sorry for this basic error. Now, it is running…

Sincerely,

Eduardo