[gmx-users] itp file

[Justin A. Lemkul]

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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-- 
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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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