# Additive forcefield of Charmm36 **URL:** \ **Category:** User discussions\ **Created:** [July 14, 2020, 8:32am UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489 "2020-07-14T08:32:12Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![Soumya](https://avatars.discourse-cdn.com/v4/letter/s/ea5d25/32.png) [@Soumya](https://gromacs.bioexcel.eu/u/Soumya)\ **Post date:** [July 14, 2020, 8:32am UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489/1 "2020-07-14T08:32:12Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hi, I am trying to setup a simulation that contains N-acetyl glucosamine (NAG).I have found the parameters in toppar\_c36\_feb16.tgz. I extracted it under the folder of Charmm36. I run the protein pdb2gmx, then include the location of the parameter file in the topology file that is generated. While adding ions I get errors like : ERROR 2314 [file par\_all36\_carb.prm, line 2572]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) ERROR 2325 [file par\_all36\_carb.prm, line 2584]: Not enough parameters ERROR 2326 [file par\_all36\_carb.prm, line 2584]: Unknown bond\_atomtype NONBONDED Could anyone please direct me towards the step by step procedure of setting up this simulation? Thanks, Soumya ---
**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:** [July 14, 2020, 3:27pm UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489/2 "2020-07-14T15:27:51Z")
You can’t use CHARMM files as input for GROMACS. Everything you need should be in our C36 port for GROMACS: [http://mackerell.umaryland.edu/charmm\_ff.shtml#gromacs](http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) ---
**Author:** ![bhaddad](https://avatars.discourse-cdn.com/v4/letter/b/7ba0ec/32.png) [@bhaddad](https://gromacs.bioexcel.eu/u/bhaddad)\ **Post date:** [September 22, 2020, 2:45am UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489/3 "2020-09-22T02:45:19Z")
In a similar vein, I am attempting to acetylate the N-terminus of my protein using **charmm36-jul2020.ff** and I continuously run into a fatal error when I run `gmx pdb2gmx -f input.pdb -o test -ter` Fatal error: Residue 2 named ACE of a molecule in the input file was mapped to an entry in the topology database, but the atom C used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. This is the section in merged.rtp that pertains to ACE: 114194 [ACE] ; N-terminal acetyl patch 114195 [atoms] 114196 CAY CT3 -0.270 1 114197 HY1 HA3 0.090 1 114198 HY2 HA3 0.090 1 114199 HY3 HA3 0.090 1 114200 CY C 0.510 1 114201 OY O -0.510 1 114202 [bonds] 114203 CY CAY 114204 CY +N 114205 CAY HY1 114206 CAY HY2 114207 CAY HY3 114208 OY CY 114209 [impropers] 114210 CY CAY +N OY And here is a sample from the .pdb I am using as input for pdb2gmx: REMARK original generated coordinate pdb file ATOM 1 CAY ACE A 2 7.298 -5.939 -34.996 1.00 0.00 AP1 ATOM 2 HY1 ACE A 2 8.027 -6.594 -34.796 1.00 0.00 AP1 ATOM 3 HY2 ACE A 2 6.639 -6.345 -35.630 1.00 0.00 AP1 ATOM 4 HY3 ACE A 2 6.837 -5.673 -34.149 1.00 0.00 AP1 ATOM 5 CY ACE A 2 7.698 -5.126 -35.419 1.00 0.00 AP1 ATOM 6 OY ACE A 2 6.969 -4.471 -35.618 1.00 0.00 AP1 ATOM 7 N GLY A 2 8.687 -5.251 -35.494 1.00 0.00 AP1 N ATOM 8 HN GLY A 2 9.416 -5.906 -35.294 1.00 0.00 AP1 ATOM 9 CA GLY A 2 9.267 -4.071 -36.107 1.00 0.00 AP1 C ---
**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:** [September 22, 2020, 6:26pm UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489/4 "2020-09-22T18:26:47Z")
Please provide the full screen output of `pdb2gmx`, including all selections you have made. ---
**Author:** ![bhaddad](https://avatars.discourse-cdn.com/v4/letter/b/7ba0ec/32.png) [@bhaddad](https://gromacs.bioexcel.eu/u/bhaddad)\ **Post date:** [September 22, 2020, 6:45pm UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489/5 "2020-09-22T18:45:45Z")
(base) [bassam@maxwell Cx46]$ gmx pdb2gmx -f ProtLip.pdb -o TEST -ff charmm36-jul2020 -water tip3p -ter :-) GROMACS - gmx pdb2gmx, 2020 (-: ``` GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd ``` Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright © 1991-2000, University of Groningen, The Netherlands. Copyright © 2001-2019, 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 pdb2gmx, version 2020 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /data/gromacs\_tutorial/Cx46 Command line: gmx pdb2gmx -f ProtLip.pdb -o TEST -ff charmm36-jul2020 -water tip3p -ter Using the Charmm36-jul2020 force field in directory charmm36-jul2020.ff going to rename charmm36-jul2020.ff/merged.r2b Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-jul2020.ff/merged.r2b Reading ProtLip.pdb… Read ‘’, 163320 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 13 chains and 0 blocks of water and 3420 residues with 163320 atoms chain #res #atoms 1 ‘A’ 197 3226 2 ‘B’ 197 3226 3 ‘C’ 197 3226 4 ‘D’ 197 3226 5 ‘E’ 197 3226 6 ‘F’ 197 3226 7 ‘G’ 197 3226 8 ‘H’ 197 3226 9 ‘I’ 197 3226 10 ‘J’ 197 3226 11 ‘K’ 197 3226 12 ‘L’ 197 3226 13 ‘M’ 1056 124608 WARNING: there were 1 atoms with zero occupancy and 0 atoms with occupancy unequal to one (out of 163320 atoms). Check your pdb file. Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-jul2020.ff/atomtypes.atp Reading residue database… (Charmm36-jul2020) Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-jul2020.ff/merged.rtp Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-jul2020.ff/merged.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-jul2020.ff/merged.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-jul2020.ff/merged.c.tdb Back Off! I just backed up topol.top to ./#topol.top.1# Processing chain 1 ‘A’ (3226 atoms, 197 residues) Identified residue ACE2 as a starting terminus. Identified residue TRP224 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS54 CYS61 CYS65 MET102 CYS178 CYS183 CYS189 SG832 SG925 SG980 SD1617 SG2471 SG2555 SG2635 CYS61 SG925 0.541 CYS65 SG980 0.494 0.354 MET102 SD1617 5.869 6.005 5.749 CYS178 SG2471 0.683 0.498 0.204 5.696 CYS183 SG2555 0.690 0.203 0.336 5.925 0.400 CYS189 SG2635 0.203 0.548 0.419 5.886 0.575 0.665 MET204 SD2898 2.688 3.082 2.790 3.916 2.799 3.097 2.684 CYS209 SG2967 3.217 3.532 3.189 3.942 3.129 3.501 3.142 MET204 SD2898 CYS209 SG2967 1.183 Linking CYS-54 SG-832 and CYS-189 SG-2635… Linking CYS-61 SG-925 and CYS-183 SG-2555… Linking CYS-65 SG-980 and CYS-178 SG-2471… Select start terminus type for ACE-2 0: NH3+ 1: NH2 2: 5TER 3: None 3 Start terminus ACE-2: None Select end terminus type for TRP-224 0: COO- 1: COOH 2: CT2 3: 3TER 4: None 0 End terminus TRP-224: COO- Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-jul2020.ff/merged.arn Checking for duplicate atoms… Generating any missing hydrogen atoms and/or adding termini. * * * Program: gmx pdb2gmx, version 2020 Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 151) Fatal error: Residue 2 named ACE of a molecule in the input file was mapped to an entry in the topology database, but the atom C used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. ## 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) (base) [bassam@maxwell Cx46]$ ---
**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:** [September 22, 2020, 7:03pm UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489/6 "2020-09-22T19:03:33Z")
Since the amino acids each define an improper requiring the C atom of the previous residue (i.e. `-C`), a fatal error is issued if using CHARMM nomenclature. We changed the ACE `.rtp` entry to be consistent with CHARMM, hoping it would enable better compatibility with CHARMM-prepared coordinates, but clearly that was a mistake. Replace your `ACE` entry in `merged.rtp` with this one: ``` [ACE] ; terminal residue, provided by Mark Abraham [atoms] CH3 CT3 -0.270 1 HH31 HA3 0.090 1 HH32 HA3 0.090 1 HH33 HA3 0.090 1 C C 0.510 2 O O -0.510 2 [bonds] C CH3 C +N CH3 HH31 CH3 HH32 CH3 HH33 O C [impropers] C CH3 +N O ``` And rename atoms in the PDB file accordingly. ---
**Author:** ![bhaddad](https://avatars.discourse-cdn.com/v4/letter/b/7ba0ec/32.png) [@bhaddad](https://gromacs.bioexcel.eu/u/bhaddad)\ **Post date:** [September 22, 2020, 8:05pm UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489/7 "2020-09-22T20:05:41Z")
Thank you for the response. I seemed to have created another problem by doing so. Fatal error: The residues in the chain ACE2–TRP224 do not have a consistent type. The first residue has type ‘Protein’, while residue C S54 is of type ‘Other’. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory. If there are other molecules such as ligands, they should not have the same chain ID as the adjacent protein chain since it’s a separate molecule. I assume this comes from the .pdb, when changing the names as recommended it messed up the pdbfile. ``` 1 REMARK original generated coordinate pdb file 2 ATOM 1 CH3 ACE A 2 7.298 -5.939 -34.996 1.00 0.00 AP1 3 ATOM 2 HH31ACE A 2 8.027 -6.594 -34.796 1.00 0.00 AP1 4 ATOM 3 HH32ACE A 2 6.639 -6.345 -35.630 1.00 0.00 AP1 5 ATOM 4 HH33ACE A 2 6.837 -5.673 -34.149 1.00 0.00 AP1 6 ATOM 5 C ACE A 2 7.698 -5.126 -35.419 1.00 0.00 AP1 7 ATOM 6 O ACE A 2 6.969 -4.471 -35.618 1.00 0.00 AP1 8 ATOM 7 N GLY A 2 8.687 -5.251 -35.494 1.00 0.00 AP1 N 9 ATOM 8 HN GLY A 2 9.416 -5.906 -35.294 1.00 0.00 AP1 ``` Add a space between the atom-name and residue-name ---
**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:** [September 22, 2020, 8:20pm UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489/8 "2020-09-22T20:20:18Z")
I’m guessing you replaced “CY” by "C " globally in the file, which turns all “CYS” residues into “C S.” You need to fix that or go back to the original file and be more judicious in your choice of replacement string. ---
**Author:** ![bhaddad](https://avatars.discourse-cdn.com/v4/letter/b/7ba0ec/32.png) [@bhaddad](https://gromacs.bioexcel.eu/u/bhaddad)\ **Post date:** [September 22, 2020, 9:29pm UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489/9 "2020-09-22T21:29:27Z")
**Thank you for catching that!** Unfortunately pdb2gmx was still throwing up some errors about the hydrogens so I used the `-ignh` flag. While this allowed me to construct the topology files, I am wondering if this will have any negative impact on their new assignments. ---
**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:** [September 23, 2020, 1:34am UTC](https://gromacs.bioexcel.eu/t/additive-forcefield-of-charmm36/489/10 "2020-09-23T01:34:52Z")
The H atoms are reconstructed in their ideal positions relative to the constructing heavy atoms. I doubt there’s a major difference but you can always compute an RMSD between the structures to see. Within a few steps of MD, the differences will go out the window.