[gmx-users] GROMOS96 topology for small molecule

[mohsen ramezanpour]

It is on now,you can use it.
as Justin said you should validate it.
best

On Tue, Jan 18, 2011 at 9:37 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> C.Y. Chang wrote:
>
>> Hi,
>>
>> I need to obtain the GROMOS96 topology files (and including the
>> corresponding PDB files)  for some small molecules.
>> I could obtain them from PRODRG beta server before, but the server seems
>> to shut down now.
>>
>
> According to the site, it will be up within 24 hours.  PRODRG is a fine
> tool, but should not be viewed as sufficient to produce reliable topologies
> in the absence of further validation and almost certain refinement.
>
>
>  How could I get them? or from other server or program?
>>
>
> Regardless of how you produce your topologies, you should understand the
> intrinsics of the force field so you can do proper validation.
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
>
> Pay special attention to the second link and the referenced material.
>
> -Justin
>
>
>>                                                     Chia-yun Chang
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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