Rebeca García Fandiño wrote:
Hello,
I don´t understand the correction I should do from itp.
I have removed from the urea original urea.itp these lines,
don't use this model. do a proper literature search.
#ifdef Boek
1 C 1 UREA C1 1 0.38
2 O 1 UREA O2 1 -0.38
3 NT 1 UREA N3 2 -0.83
4 H 1 UREA H4 2 0.415
5 H 1 UREA H5 2 0.415
6 NT 1 UREA N6 3 -0.83
7 H 1 UREA H7 3 0.415
8 H 1 UREA H8 3 0.415
#else
#endif[ moleculetype ]
so now, my urea.itp file is:
; name nrexcl
Urea 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 C 1 UREA C1 1 0.683
2 O 1 UREA O2 1 -0.683
3 NT 1 UREA N3 2 -0.622
4 H 1 UREA H4 2 0.346
5 H 1 UREA H5 2 0.276
6 NT 1 UREA N6 3 -0.622
7 H 1 UREA H7 3 0.346
8 H 1 UREA H8 3 0.276
[ bonds ]
; ai aj funct b0 kb
3 4 1 1.000000e-01 3.744680e+05
3 5 1 1.000000e-01 3.744680e+05
6 7 1 1.000000e-01 3.744680e+05
6 8 1 1.000000e-01 3.744680e+05
1 2 1 1.230000e-01 5.020800e+05
1 3 1 1.330000e-01 3.765600e+05
1 6 1 1.330000e-01 3.765600e+05
[ pairs ]
; ai aj funct c6 c12
2 4 1 0.000000e+00 0.000000e+00
2 5 1 0.000000e+00 0.000000e+00
2 7 1 0.000000e+00 0.000000e+00
2 8 1 0.000000e+00 0.000000e+00
3 7 1 0.000000e+00 0.000000e+00
3 8 1 0.000000e+00 0.000000e+00
4 6 1 0.000000e+00 0.000000e+00
5 6 1 0.000000e+00 0.000000e+00
[ angles ]
; ai aj ak funct th0 cth
1 3 4 1 1.200000e+02 2.928800e+02
1 3 5 1 1.200000e+02 2.928800e+022 1 6 1 1.215000e+02 5.020800e+02
3 1 6 1 1.170000e+02 5.020800e+02
[ dihedrals ]
; ai aj ak al funct phi cp mult
2 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
6 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
2 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00
6 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00
2 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00
3 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00
2 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
3 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
[ dihedrals ]
; ai aj ak al funct q0 cq
3 4 5 1 2 0.000000e+00 1.673600e+02
6 7 8 1 2 0.000000e+00 1.673600e+02
1 3 6 2 2 0.000000e+00 1.673600e+02
4 3 5 1 1.200000e+02 3.347200e+02
1 6 7 1 1.200000e+02 2.928800e+02
1 6 8 1 1.200000e+02 2.928800e+02
7 6 8 1 1.200000e+02 3.347200e+02
2 1 3 1 1.215000e+02 5.020800e+02
Following Chapter 5 in the manual (page 102), the file described for
urea.itp is the same as mine. For the topology (page 103)
#include "ffgmx.itp" is used, but I don´t see any more different.
With this modification in the urea.itp I get the same error. Any idea of
what could be the problem?
Thank you very much for your help,
Rebeca Garcia
Parc Cientific de Barcelona
rega...@hotmail.com <mailto:rega...@hotmail.com>
> Date: Thu, 18 Dec 2008 09:21:41 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Urea topology problem
>
>
>
> Rebeca García Fandiño wrote:
>
> <snip>
>
> >
> > ERROR 1 [file solvated.top, line 39]:
> >
> > atom C1 (Res UREA-1) has mass 0
> >
> >
>
> In urea.itp, no masses are defined. If you correct the format of this
file (see
> Chapter 5 of the manual), then this issue should be resolved.
>
>
> >
> > Which force field does this urea.itp correspond to? Where should it
look
> > for the atomtypes of urea?
> >
> >
>
> The .atp file corresponding to the force field you are using
(ffG43a2). The
> atomtypes for urea appear to be generic for use with the Gromos96
force fields.
> There are specific atomtypes within ffG53a6 for urea, if you want to
use the
> newer force field (check the ffG53a6.rtp file for the urea parameters).
>
> -Justin
>
>
> >
> > Thank you very much for your help,
> >
> >
> >
> > Rebeca Garcia
> >
> > Parc Cientific de Barcelona
> >
> > rega...@hotmail.com
> >
> >
> >
------------------------------------------------------------------------
> > ¿Aún no tienes Internet Explorer 7? Bájatelo y consigue un regalo
gratis
> > <http://vivelive.com/ieak7/>
> >
> >
> >
------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
Descárgate gratis el nuevo Windows Live Messenger
<http://download.live.com/>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
