[gmx-users] Creating Custom .rtp files
Momin Ahmad
momin.ahmad at kit.edu
Wed Aug 2 11:07:18 CEST 2017
I think the reason for the weird log is the "|&tee" command that lets
you write the output of another command into a file. In the case of the
error i could choose the forcefield before the error occurred. The
methane was called "CH4" before, i just changed the names for
troubleshooting. This time i did copy&paste manually. Files are
attached. There are two comments that show the differences in the
versions. Again: the two .rtp files for both versions are identical and
the same .pdb file is used.
Am 01.08.2017 um 20:42 schrieb Justin Lemkul:
>
>
> On 8/1/17 10:32 AM, Momin Ahmad wrote:
>> please finde the files attached to this email: log-files for the
>> 5.1.2 version and the 2016.3 version, also again the .rtp file and
>> the .pdb file
>>
>
> The screen output seems garbled to me, with the fatal error coming
> before the force field selection, and multiple locations being used.
> I can't figure out what's going on. Your .rtp needs to be in the
> force field directory that you choose, either locally (within the
> working directory) or system-wide (wherever that is installed). Note
> also that "CH4" and "CH41" are different, because one error indicates
> that pdb2gmx finds CH4 when your .rtp is clearly CH41.
>
> -Justin
>
>>
>> Am 01.08.2017 um 00:48 schrieb Justin Lemkul:
>>>
>>>
>>> On 7/31/17 7:47 AM, Momin Ahmad wrote:
>>>> Hello,
>>>>
>>>> the .rtp file is located in the same directory as the force-field.
>>>> When i type gmx gmx2pdb ..... then the log shows that the right
>>>> path is considered and loads the needed .rtp fiels that already
>>>> exist in the forc-field file. But my custom one is ignored.
>>>>
>>>
>>> Please post the full screen output of pdb2gmx, including the force
>>> field selection. If your .rtp file is not being read, it is likely
>>> misformatted, in which case you should either write your new residue
>>> entries in an existing file or upload it to a file-sharing service
>>> so we can provide feedback.
>>>
>>> -Justin
>>>
>>>> Greets
>>>> Momin Ahmad
>>>>
>>>> Am 25.07.2017 um 16:34 schrieb RAHUL SURESH:
>>>>> On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad <momin.ahmad at kit.edu>
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I created a custom .pdb file and the associated .rtp file for the
>>>>>> force-field (amber99sb-ildn.ff). The command pdb2gmx works fine
>>>>>> for the
>>>>>> 5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3
>>>>>> version is a local installation in my /home/user folder. The log
>>>>>> shows
>>>>>> the correct paths but does not consider my custom .rtp file.
>>>>> I would recommend to check whether the rtp file location and
>>>>> source where
>>>>> gmx you have installed match. Apart from that I do not think any
>>>>> error
>>>>> with version of Gromacs.
>>>>>
>>>>>> Am i doing
>>>>>> something wrong with the newer version? I added two simple files
>>>>>> of my
>>>>>> problem. Thanks in advance.
>>>>>>
>>>>>> Cheers
>>>>>> Momin Ahmad
>>>>>> Karlsruher Institut of Technology
>>>>>> Germany
>>>>>> --
>>>>>> 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
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>> or
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>>>>
>>>
>>
>>
>>
>
--
Momin Ahmad
Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: Momin.Ahmad at kit.edu
-------------- next part --------------
:-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:
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 5.1.2
Executable: /usr/bin/gmx
Data prefix: /usr
Command line:
gmx pdb2gmx -f methane.pdb
Select the Force Field:
From '/usr/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: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6
Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
Select the Water Model:
1: TIP3P TIP 3-point, recommended
2: TIP4P TIP 4-point
3: TIP4P-Ew TIP 4-point optimized with Ewald
4: TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
5: SPC simple point charge
6: SPC/E extended simple point charge
7: None
7
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b
Reading methane.pdb...
Read 'METHANE', 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 ' ' 1 5
All occupancies are one
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
Atomtype 67
Reading residue database... (amber99sb-ildn)
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/methane.rtp //COMMENT: NOW GMX 5.1.2 DOES LOAD MY CUSTOM .rtp FILE? WHY NOT 2016.3?
Residue 110
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
Residue 126
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.3#
Processing chain 1 (5 atoms, 1 residues)
Warning: Starting residue CH41 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/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 5 atoms
Making bonds...
Number of bonds was 4, now 4
Generating angles, dihedrals and pairs...
Making cmap torsions...
There are 0 dihedrals, 0 impropers, 6 angles
0 pairs, 4 bonds and 0 virtual sites
Total mass 16.042 a.m.u.
Total charge 0.000 e
Writing topology
Back Off! I just backed up posre.itp to ./#posre.itp.1#
Writing coordinate file...
Back Off! I just backed up conf.gro to ./#conf.gro.1#
--------- PLEASE NOTE ------------
You have successfully generated a topology from: methane.pdb.
The Amber99sb-ildn force field is used.
--------- ETON ESAELP ------------
gcq#213: "Everybody is Smashing Things Down" (Offspring)
-------------- next part --------------
:-) GROMACS - gmx pdb2gmx, 2016.3 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra 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) 2001-2017, 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 2016.3
Executable: /home/bromin/gromacs-2016.3/bin/gmx
Data prefix: /home/bromin/gromacs-2016.3
Working dir: /data/click-chemistry/test
Command line:
gmx pdb2gmx -f methane.pdb
Select the Force Field:
From '/home/bromin/gromacs-2016.3/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: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6
Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
Select the Water Model:
1: TIP3P TIP 3-point, recommended
2: TIP4P TIP 4-point
3: TIP4P-Ew TIP 4-point optimized with Ewald
4: TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
5: SPC simple point charge
6: SPC/E extended simple point charge
7: None
7
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/dna.r2b
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/rna.r2b
Reading methane.pdb...
Read 'METHANE', 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 ' ' 1 5
All occupancies are one
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
Atomtype 67
Reading residue database... (amber99sb-ildn)
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
//COMMENT: WHY IS methane.rtp NOT LOADING?! IT IS LOCATED in /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/
Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 (5 atoms, 1 residues)
Warning: Starting residue CH41 in chain not identified as Protein/RNA/DNA. //COMMENT: WHY IS CH41 WRITTEN HERE? NO FILE MENTIONS CH41!
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
-------------------------------------------------------
Program: gmx pdb2gmx, version 2016.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 649)
Fatal error:
Residue 'CH4' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
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