Additive forcefield of Charmm36

User discussions
1

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

2

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

3

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

4

Please provide the full screen output of pdb2gmx, including all selections you have made.

5

(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 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

(base) [bassam@maxwell Cx46]$

6

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.

7

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

8

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.

9

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.

10

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.