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

Justin Lemkul jalemkul at vt.edu
Fri Mar 29 02:47:03 CET 2019 


On 3/28/19 9:30 PM, Tingguang.S wrote:
> 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

I strongly encourage you to upgrade to a more recent version of GROMACS. 
The 5.1 series is deprecated.

In any case, it's not actually terminal patching that is the issue. It 
is the merged.arn file renaming your H atom, because normally "H" in a 
PDB file needs to be "HN" for CHARMM. Comment out the only line in 
merged.arn and re-run pdb2gmx. Just don't forget to uncomment the line 
before trying to process any proteins.

-Justin

> 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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>>>> Gromacs Users mailing list
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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!
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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

==================================================

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