[gmx-users] itp file

[Justin A. Lemkul]

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?

> appreciate if you give the address of the related page of the website??  

 From the homepage: Downloads -> User Contributions -> Other software

> 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.

-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

========================================