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 <p...@uab.edu>
>Para: Discussion list for GROMACS users <gmx-users@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@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-requ...@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
>p...@uab.edu | Birmingham AL 35294-4461
>(205) 690-0808 |
>==================================================================
>
>--
>gmx-users mailing list gmx-users@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-requ...@gromacs.org.
>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
