[gmx-users] Re: bypassing pdb2gmx

[Amit Choubey]

thanks a bunch for the input.

On Thu, Sep 10, 2009 at 9:38 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Amit Choubey wrote:
>
>> hi everyone,
>>
>> I guess if i knew the exact format of .gro files i could write a small
>> code to copy data from pdb to gro . I cannot find this info anywhere. I
>> believe that it has co-ordinates and velocities but how are the velocities
>> choose (randomly?). I am also not sure abt the exact order.
>>
>>
> The format is available as part of the online manual:
>
> http://manual.gromacs.org/current/online/gro.html
>
> Although I don't know why you feel it necessary to write code that's
> already part of editconf.
>
> Velocities are assigned randomly when grompp sees "gen_vel = yes" in the
> .mdp file, according to the gen_temp parameter.  I'd say keep life easy and
> use the functions Gromacs already provides you instead of writing code for
> converting coordinates and writing velocities :)
>
> -Justin
>
>  Amit
>>
>> On Wed, Sep 9, 2009 at 5:29 PM, Amit Choubey <kgp.amit at gmail.com <mailto:
>> kgp.amit at gmail.com>> wrote:
>>
>>    hi everyone,
>>
>>    I have a pdb file of my system and i want it to be fed into the
>>    GROMACS software. I have a new force field for the simulation and i
>>    have made the .top file manually which includes the new library FF
>>    files. I need to get a .gro file from the .pdb file that i have. So,
>>    is there a way out to do this without incorporating pdb2gmx because
>>    i dont use the standard FF and i dont really have all the other
>>    datafiles for the new FF except for necessary bond and nonbonded infos.
>>
>>    Amit
>>
>>
>>
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>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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