[gmx-users] GROMOS96 topology for small molecule

[Justin A. Lemkul]

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
> 

-- 
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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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