[gmx-users] NBFIX to gromacs

[Ricardo O. S. Soares]

Dear Mr. Lai,

I see. I'll look more deeply into it, thanks for your answer.

Ricardo.
 





>________________________________
> De: Peter C. Lai <pcl at uab.edu>
>Para: Ricardo O. S. Soares <ross_usp at yahoo.com.br>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
>Enviadas: Quarta-feira, 2 de Maio de 2012 20:35
>Assunto: Re: [gmx-users] NBFIX to gromacs
> 
>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.
>> >
>> >> -- 
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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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>
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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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