[gmx-users] itp file

[Jamie Seyed]

Hi Justin,
I used opls and I already tried PRODRG, but it did not help... I appreciate
if you give the address of the related page of the website??  because I
really problems to open some parts of the gromacs website. If non of them
help, should I use molden myself to find all the entries???
Thank you very much for any suggestion.

On Sat, Aug 8, 2009 at 4:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Jamie Seyed wrote:
>
>> Dear gmx users,
>> I need some help for generating a itp file for my molecular structure. I
>> am using molden and now I have the xyz and pdb files. I read through mailing
>> list but seems I should provide itp myself. But I don't know the right way
>> to do that. Is it using molden and find one-by-one bond sand angles and
>> dihedrals... . If I have already the itp file for a part of molecule is it
>> only to add the information of new atoms to the old itp file?? I will really
>> appreciate it if someone gives me better ideas and more related information
>> to make my itp file.
>>
>>
>
> Depending on the force field you want to use, there are various scripts in
> the User Contributions section of the Gromacs site.  The PRODRG server is
> also useful for generating an initial topology, but the charges and charge
> groups it assigns are often unsatisfactory and require manual adjustment.
>
> -Justin
>
>  Many Thanks in Advance,
>> Jamie
>>
>>
>> ------------------------------------------------------------------------
>>
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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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