[gmx-users] NBFIX to gromacs

[Peter C. Lai]

The problem is that functype 1 for [ pairtypes ] when gromacs uses a CHARMM
forcefield is that gromacs treats them as 1-4 interactions. You will have to 
ask/wait for someone familiar with the gromacs source to say if there is a 
different functype available to use to override non-1-4 interactions with
the given pair parameters that you want to specify.


On 2012-05-02 12:35:17PM -0700, Ricardo O. S. Soares wrote:
> Dear Mr. Peter C. Lai,
> 
> I appreciate your kind response.
> 
> I apologize for the delay on my part.
> This NBFIX parameters that I'm working with came from the str file in http://terpconnect.umd.edu/~jbklauda/research/download/chol_new.str , which dates from 2012.
> I successfully converted this whole file, now I'm wondering about this NBFIX section.
> I'm thinking about converting these values from Kcal to KJ and Angstrom to nm, adapt and append to [ pairtypes ]. Could this be the right move?
> Thanks again,
> 
> Ricardo.
> 
> 
> 
> 
> 
> 
> >________________________________
> > De: Peter C. Lai <pcl at uab.edu>
> >Para: Discussion list for GROMACS users <gmx-users at gromacs.org> 
> >Enviadas: Segunda-feira, 30 de Abril de 2012 20:46
> >Assunto: Re: [gmx-users] NBFIX to gromacs
> > 
> >NBFIXes haven't been used in charmm for a long time (1998), although 
> >current versions still read topologies containing those records. Perhaps you 
> >should reparameterize your molecule with a more current version? (Or start with
> >the coordinate file and use pdb2gmx with the converted ff). The only thing I
> >can think of if you really need to do it is to create new atom types.
> >As far as I know, gromacs only supports 1 set of vdw coefficients and a 1-4
> >pair.
> >
> >
> >
> >On 2012-04-30 01:30:59PM -0700, Ricardo O. S. Soares wrote:
> >> Hello GMX users,
> >> 
> >> does anyone that dealt with Charmm before knows how to translate the NBFIX section into a Gromacs ff format? After convertion from KCal to KJ, does it go into [pairtypes]?
> >> I see that it concerns to corrections in LJ interactions, however the charmm documentation seems a bit unclear to me.
> >> 
> >> Thanks again,
> >>  Ricardo.
> >
> >> -- 
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the 
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> >-- 
> >==================================================================
> >Peter C. Lai            | University of Alabama-Birmingham
> >Programmer/Analyst        | KAUL 752A
> >Genetics, Div. of Research    | 705 South 20th Street
> >pcl at uab.edu            | Birmingham AL 35294-4461
> >(205) 690-0808            |
> >==================================================================
> >
> >-- 
> >gmx-users mailing list    gmx-users at gromacs.org
> >http://lists.gromacs.org/mailman/listinfo/gmx-users
> >Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >Please don't post (un)subscribe requests to the list. Use the 
> >www interface or send it to gmx-users-request at gromacs.org.
> >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> >

> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
==================================================================