[gmx-users] GROMOS96 topology for small molecule

[C.Y. Chang]

thanks :)

2011/1/19 mohsen ramezanpour <ramezanpour.mohsen at gmail.com>

> 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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>
>
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