[gmx-users] How to create top of small molecules with pdb2gmx

Fri Mar 29 02:30:38 CET 2019

The pdb file for formic acid is:

ATOM      1  C   FORH    1      -4.360   0.340  -0.050  0.00  0.00
ATOM      2  H   FORH    1      -5.450   0.260  -0.050  0.00  0.00
ATOM      3  O2  FORH    1      -3.790   1.370  -0.050  0.00  0.00
ATOM      4  O1  FORH    1      -3.730  -0.830  -0.050  0.00  0.00
ATOM      5  HO1 FORH    1      -4.350  -1.550  -0.050  0.00  0.00

The output of the pdb2gmx is:

GROMACS:      gmx pdb2gmx, VERSION 5.1.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx pdb2gmx -f formic-acid.pdb -ter

Select the Force Field:
From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: CHARMM36 all-atom force field (November 2018)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
9

Using the Charmm36-nov2018 force field in directory charmm36-nov2018.ff

Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/watermodels.dat

Select the Water Model:
 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H
 2: TIP4P TIP 4-point
 3: TIP5P TIP 5-point
 4: SPC simple point charge
 5: SPC/E extended simple point charge
 6: None
6
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.r2b
Reading formic-acid.pdb...
Read 5 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 5 atoms

  chain  #res #atoms
  1 'X'     1      5  

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/atomtypes.atp
Atomtype 447
Reading residue database... (charmm36-nov2018)
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.rtp
Residue 1318
Sorting it all out...
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 'X' (5 atoms, 1 residues)
Warning: Starting residue FORH1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.arn

-------------------------------------------------------
Program gmx pdb2gmx, VERSION 5.1.4
Source code file: /home/chengqianwei/program/gromacs-5.1.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 746

Fatal error:
Atom HN in residue FORH 1 was not found in rtp entry FORH with 5 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

From: Justin Lemkul <jalemkul at vt.edu>
Date: 2019-03-29 09:16:59
To:  gmx-users at gromacs.org
Subject: Re: [gmx-users] How to create top of small molecules with pdb2gmx>
>
>On 3/28/19 9:03 PM, Tingguang.S wrote:
>> Thank you Justin,
>>
>>
>> I had tried many times, and the interactive selection still didn't work, I really need help. I downloaded charmm36-nov2018.ff.tgz from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs,  and extracted it into /usr/local/gromacs/share/gromacs/top.
>>
>>
>> I had attached the log file, and pdb file of formic acid. Please help with this.
>
>The mailing list does not accept attachments. Please post files to a 
>file-sharing service and provide a URL.
>
>-Justin
>
>>
>> Thank you for your time!
>>
>>
>>
>>
>> 发件人：Justin Lemkul <jalemkul at vt.edu>
>> 发送日期：2019-03-28 21:48:32
>> 收件人：gmx-users at gromacs.org
>> 主题：Re: [gmx-users] How to create top of small molecules with pdb2gmx>
>>> On 3/28/19 9:36 AM, Tingguang.S wrote:
>>>> Thank you, Justin！
>>>>
>>>>
>>>> You mean that I should use the following command:  "gmx pdb2gmx -f formic-acid.pdb -ter "？
>>>> I had used the flag -ter, but the program did not prompt interactive selection.
>>> I don't know how that could have happened. The purpose of -ter is to
>>> trigger an interactive selection.
>>>
>>> -Justin
>>>
>>> -- 
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Office: 301 Fralin Hall
>>> Lab: 303 Engel Hall
>>>
>>> Virginia Tech Department of Biochemistry
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==================================================
>>>
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>>
>>
>>
>>
>>
>>
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Assistant Professor
>Office: 301 Fralin Hall
>Lab: 303 Engel Hall
>
>Virginia Tech Department of Biochemistry
>340 West Campus Dr.
>Blacksburg, VA 24061
>
>jalemkul at vt.edu | (540) 231-3129
>http://www.thelemkullab.com
>
>==================================================
>
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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