[gmx-users] NBFIX to gromacs
Ricardo O. S. Soares
ross_usp at yahoo.com.br
Wed May 2 21:35:17 CEST 2012
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?
> 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
>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,
>> gmx-users mailing list gmx-users at gromacs.org
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>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 |
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