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.
Thank you for your time!
发件人：Justin Lemkul <jalem...@vt.edu>
发送日期：2019-03-28 21:48:32
收件人：gmx-us...@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.
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[chengqianwei@localhost test2]$ gmx pdb2gmx -f formic-acid.pdb -ter
:-) GROMACS - gmx pdb2gmx, VERSION 5.1.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, 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 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
-------------------------------------------------------
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