[gmx-users] Merging different topology files
Momin Ahmad
momin.ahmad at kit.edu
Fri Sep 8 11:50:22 CEST 2017
Thank you for your help. I already did that but i get a weird error that
i can not solve. I attached the topology files and the error message.
Maybe the numbering of the residues has to be changed? Thanks in advance.
Cheers,
Momin
Am 07.09.2017 um 21:08 schrieb Justin Lemkul:
>
>
> On 9/7/17 10:19 AM, Momin Ahmad wrote:
>> Hello all,
>>
>> is there a simple way to merge two or more topology files into one? I
>> am trying to use grompp to set up a simulation but my solvation
>> contains different molecules which have different .top files. I also
>> tried creating a main topology file which includes the other two
>> topologies but without success. Hope anyone knows how to solve this.
>>
>
> The #include mechanism is the only way to do this. If you have two
> .top (system topology) files, then:
>
> 1. Remove any #include statement for a parent force field (i.e. the
> file with [defaults] in it)
> 2. Remove any [system] or [molecules] directive
>
> (you now have proper .itp format)
>
> 3. Remove any redundant #include statements (e.g. for water, ions) to
> avoid "moleculetype redefined" errors
> 4. Construct a new .top that #includes a parent force field, your two
> new .itp files, and has [system] and [molecules] directives.
>
> -Justin
>
-------------- next part --------------
:-) GROMACS - gmx grompp, 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 grompp, version 2016.3
Executable: /usr/local/bin/gmx
Data prefix: /usr/local
Working dir: /home/momin/work/click-chemistry/simulation
Command line:
gmx grompp -f minim.mdp -c system_solv.gro -p topol.top -o system.tpr
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#
NOTE 1 [file minim.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 61641030
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
ERROR 1 [file methane_custom.itp, line 16]:
No default Bond types
ERROR 2 [file methane_custom.itp, line 17]:
No default Bond types
ERROR 3 [file methane_custom.itp, line 18]:
No default Bond types
ERROR 4 [file methane_custom.itp, line 19]:
No default Bond types
ERROR 5 [file methane_custom.itp, line 23]:
No default Angle types
ERROR 6 [file methane_custom.itp, line 24]:
No default Angle types
ERROR 7 [file methane_custom.itp, line 25]:
No default Angle types
ERROR 8 [file methane_custom.itp, line 26]:
No default Angle types
ERROR 9 [file methane_custom.itp, line 27]:
No default Angle types
ERROR 10 [file methane_custom.itp, line 28]:
No default Angle types
WARNING 1 [file topol.top, line 18]:
Too few parameters on line (source file
/home/momin/gromacs-2016.3/src/gromacs/gmxpreprocess/toppush.cpp, line
2377)
Excluding 3 bonded neighbours molecule type 'METHANE'
WARNING 2 [file topol.top, line 19]:
Too few parameters on line (source file
/home/momin/gromacs-2016.3/src/gromacs/gmxpreprocess/toppush.cpp, line
2377)
Excluding 3 bonded neighbours molecule type 'METHANE'
-------------------------------------------------------
Program: gmx grompp, version 2016.3
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 612)
Fatal error:
number of coordinates in coordinate file (system_solv.gro, 113)
does not match topology (topol.top, 10)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
-------------- next part --------------
; main topology file
;
; Include force-field
#include "amber99sb-ildn.ff/forcefield.itp"
;Include topologies
#include "methane_custom.itp"
#include "ammonia_custom.itp"
;Include water topology
;#include "amber99sb-ildn.ff/tip4p.itp"
[ system ]
Ammonia + Methane
[molecules]
AMMONIA
METHANE
-------------- next part --------------
[ moleculetype ]
; Name nrexcl
METHANE 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 CH4 rtp CH4 q 0.0
1 C 1 CH4 C 1 -0.24 12.01 ; qtot -0.24
2 H 1 CH4 H1 1 0.06 1.008 ; qtot -0.18
3 H 1 CH4 H2 1 0.06 1.008 ; qtot -0.12
4 H 1 CH4 H3 1 0.06 1.008 ; qtot -0.06
5 H 1 CH4 H4 1 0.06 1.008 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
; Include Position restraint file
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
-------------- next part --------------
[ moleculetype ]
; Name nrexcl
AMMONIA 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 0 NH3 rtp NH3 q -0.1
1 N 01 NH3 N 1 -0.39 14.01 ; qtot -0.39
2 H 01 NH3 H1 1 0.13 1.008 ; qtot -0.26
3 H 01 NH3 H2 1 0.13 1.008 ; qtot -0.13
4 H 01 Nh3 H3 2 0.13 1.008 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
; Include Position restraint file
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
More information about the gromacs.org_gmx-users
mailing list