[gmx-users] How to create top of small molecules with pdb2gmx
Tingguang.S
tingguang.sun at gxust.edu.cn
Fri Mar 29 03:05:44 CET 2019
Thank you, Justin ! It works now.
Best regards
Sting
From: Justin Lemkul <jalemkul at vt.edu>
Date: 2019-03-29 09:46:50
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] How to create top of small molecules with pdb2gmx>
>
>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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> 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
>>>
>>> ==================================================
>>>
>>> --
>>> 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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>>
>>
>>
>
>--
>==================================================
>
>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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