# Topology file for cisplatin **URL:** \ **Category:** User discussions\ **Created:** [December 9, 2020, 7:05pm UTC](https://gromacs.bioexcel.eu/t/topology-file-for-cisplatin/1237 "2020-12-09T19:05:21Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Eduardo1](https://avatars.discourse-cdn.com/v4/letter/e/838e76/32.png) [@Eduardo1](https://gromacs.bioexcel.eu/u/Eduardo1)\ **Post date:** [December 9, 2020, 7:05pm UTC](https://gromacs.bioexcel.eu/t/topology-file-for-cisplatin/1237/1 "2020-12-09T19:05:21Z")
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 (-: ``` GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra ``` Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru 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 Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright © 1991-2000, University of Groningen, The Netherlands. Copyright © 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](http://www.gromacs.org) for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. 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](http://www.gromacs.org/Documentation/Errors) I would like to ask if anyone could help me with this error. Sincerely, Eduardo. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [December 9, 2020, 8:36pm UTC](https://gromacs.bioexcel.eu/t/topology-file-for-cisplatin/1237/2 "2020-12-09T20:36:44Z")
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. ---
**Author:** ![Eduardo1](https://avatars.discourse-cdn.com/v4/letter/e/838e76/32.png) [@Eduardo1](https://gromacs.bioexcel.eu/u/Eduardo1)\ **Post date:** [December 9, 2020, 10:55pm UTC](https://gromacs.bioexcel.eu/t/topology-file-for-cisplatin/1237/3 "2020-12-09T22:55:42Z")
Dear jalemkul, Thank you so much for your help! Sorry for this basic error. Now, it is running… Sincerely, Eduardo