[gmx-users] Creating Custom .rtp files

Momin Ahmad momin.ahmad at kit.edu
Tue Aug 1 16:32:27 CEST 2017


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


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
>>>> send a mail to gmx-users-request at gromacs.org.
>>
>

-- 
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

Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
 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
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
All occupancies are one
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp

Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp

Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp

Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/methane.rtp

Residue 110
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp

Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
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.1#
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
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

Writing coordinate file...

gcq#158: "Microsecond Here I Come" (P.J. Van Maaren)


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)

Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff


Select the Water Model:
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  

Reading residue database... (amber99sb-ildn)
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.
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 5 atoms
		--------- PLEASE NOTE ------------
You have successfully generated a topology from: methane.pdb.
The Amber99sb-ildn force field is used.
		--------- ETON ESAELP ------------
-------------- 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

Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
 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
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
All occupancies are one
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp

Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp

Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Sorting it all out...
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/dna.rtp

Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
Sorting it all out...
Opening force field file /home/bromin/gromacs-2016.3/share/gromacs/top/amber99sb-ildn.ff/rna.rtp

Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
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
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
-------------------------------------------------------

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)

Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff


Select the Water Model:
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  

Reading residue database... (amber99sb-ildn)
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.
-------------- next part --------------
[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
  1      1       3          1         1             3      1    0

; Methane
[ CH41 ]
 [ atoms ]
   C      C    -0.240     1
   H1     H     0.060     1
   H2     H     0.060     1
   H3     H     0.060     1
   H4     H     0.060     1
 [ bonds ]
   C      H1
   C      H2
   C      H3
   C      H4


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