[gmx-users] top/itp file to show parameters explicitly
Javier Cerezo
jcb1 at um.es
Mon May 21 16:10:30 CEST 2012
The actual parameters are listed in the ffbonded.itp file located in the
folder of the corresponding force field, under [ dihedraltypes ] section.
Javier
El 21/05/12 14:43, Alan escribió:
> Hi there,
>
> Is there an option in pdb2gmx that when generating the top/itp file,
> it could show the parameters explicitly? e.g.:
>
> Instead of:
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3
> 5 13 11 12 4
> 11 15 13 14 4
> 15 23 21 22 4
> 21 25 23 24 4
> 25 32 31 33 4
>
> (my hard hand modifications)
>
> [ dihedrals ] ; impropers
> ; treated as propers in GROMACS to use correct AMBER analytical function
> ; i j k l func phase kd pn
> 5 13 11 12 4 180.00 43.93200 2 ; CA-
> N- C- O
> 11 15 13 14 4 180.00 4.60240 2 ; C-
> CA- N- H
> 15 23 21 22 4 180.00 43.93200 2 ; CA-
> N- C- O
> 21 25 23 24 4 180.00 4.60240 2 ; C-
> CA- N- H
> 25 32 31 33 4 180.00 43.93200 2 ; CA-
> OC1- C- OC2
>
> I mean, if the parameters that are hiding in e.g.
> ...gromacs/top/amber99sb.ff could be showed in the top/itp file for
> human readers, that would be great.
>
> Thanks,
>
> Alan
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
>
>
>
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120521/7fb042fb/attachment.html>
More information about the gromacs.org_gmx-users
mailing list