[gmx-users] itp file

[Jamie Seyed]

On Sat, Aug 8, 2009 at 5:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> I used opls and I already tried PRODRG, but it did not help... I
>>
>
> What force field are you trying to use for your simulation?
>

I am using OPLS.


>
>
> appreciate if you give the address of the related page of the website??
>>
>
> From the homepage: Downloads -> User Contributions -> Other software
>

Ok, Thanks

>
>
> 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???
>>
>
> I don't know what you mean.  However you assign parameters must be
> consistent with the original derivation of the force field.  Whether or not
> you can do that in molden, I don't know.
>
> Between PRODRG and the contributed scripts, you should be able to write
> toplogies for Gromos, OPLS, and AMBER.

ok, I will try, Thanks.


>
> -Justin
>
>  Thank you very much for any suggestion.
>>
>> On Sat, Aug 8, 2009 at 4:56 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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 <http://vt.edu/> | (540) 231-9080
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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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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