[gmx-users] Graphene topology file

#SUKRITI GUPTA# SUKRITI002 at e.ntu.edu.sg
Fri Jul 4 09:34:54 CEST 2014 

Hi Abhijit,

My g_x2top command is:
g_x2top -f gra_2.pdb -o graphene.top -ff oplsaa -name graphene -noparam -pbc

The grompp output is:

ERROR 4100 [file graphene.top, line 10448]:      ; (for all the lines, I have copied here only one line.)
  No default Ryckaert-Bell. types

Excluding 3 bonded neighbours molecule type 'graphene'

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1987

Fatal error:
No such moleculetype SOL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Thanks
Sukriti

________________________________

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459)
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of abhijit Kayal <abhijitchemiitd at gmail.com>
Sent: Friday, July 4, 2014 2:21 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Graphene topology file

Hi Sukriti,
   Can you tell me the g_x2top command you have given and the grompp output.

Thanks
Abhijit


On Fri, Jul 4, 2014 at 10:01 AM, #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
wrote:

> Dear Justin and Abhijit,
>
> Thanks a lot for your help. Now I am able to make the topology file but
> while doing grompp for energy minimisation its not taking the dihedral
> values on its own.
>
> Regards
> Sukriti
> ________________________________
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N)
> | Nanyang Technological University
> Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive,
> Singapore(637459)
> Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
> erian.ntu.edu.sg
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of abhijit
> Kayal <abhijitchemiitd at gmail.com>
> Sent: Thursday, July 3, 2014 6:43 PM
> To: gmx-users at gromacs.org; vvchaban at gmail.com
> Subject: Re: [gmx-users] Graphene topology file
>
> Hi Sukriti,
>  Copy the oplsaa.ff directory to your working directory. Then in
> ffnonbonded.itp file add the following lines..
>  opls_995   C      6    12.01100     0.000       A    3.40000e-01
> 3.61200e-01
>  opls_996   C      6    12.01100     0.000       A    3.40000e-01
> 3.61200e-01
>  opls_997   C      6    12.01100     0.000       A    3.40000e-01
> 3.61200e-01
>
> Then in   atomname2type.n2t file add the following lines.
> C    opls_995    0      12.011  2    C  0.142  C 0.142
> C    opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
> C    opls_997    0      12.011  1    C  0.142
>
> Then use g_x2top. This will work.
>
> Thanks
>  Abhijit
>
>
> On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
> wrote:
>
> > Graphene topology is like for tube, so
> >
> > C .... C
> > C ... C ... C
> > C .... C  ....C  .... C
> >
> > to the N2T file and you are done.
> >
> >
> > Dr. Vitaly V. Chaban
> >
> >
> > On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> > >
> > >
> > > On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
> > >>
> > >> Dear all,
> > >>
> > >>
> > >> I want to simulate graphite in water, for which i am trying to create
> a
> > >> topology file for graphite. As its .rtp file cannot be written
> > correctly, i
> > >> tried to use g_x2top command following the steps given in following
> > >> tutorial.
> > >>
> > >> http://chembytes.wikidot.com/grocnt
> > >>
> > >>
> > >> But I think this tutorial is quite old and hence suitable for older
> > >> version of gromacs as it still uses FF.dat file. Moreover if i am
> > trying to
> > >> make a new forcefield directory with name graphite_oplsaa containing
> the
> > >> modified files like .n2t,.rtp and .itp, its giving me an error that
> > "Could
> > >> not find force field 'graphite_oplsaa' in current directory, install
> > tree or
> > >> GMXDATA path". When I try to add this forcefield in original path ie.
> > >> user/share/gromacs/top, it does not allow me to do that as i am not
> the
> > >> administrator. Can anyone please let me know how to create the
> topology
> > >> file. I require 3 graphene sheets with pbc. I have created the .pdb
> file
> > >> using nanobuilder in vmd.
> > >>
> > >
> > > The tutorial is indeed outdated but the logic is fairly sound.  You
> don't
> > > have to modify anything in $GMXLIB (system-wide); you can just create
> an
> > > .n2t file in the working directory and it will override the one at the
> > force
> > > field level.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
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>
> --
> Abhijit kayal
> Research Scholar
> Theoretical Chemistry
> IIT Kanpur
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--
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur
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