[gmx-users] Small organic molecules

[Justin A. Lemkul]

Stefan Frieder Hopp wrote:
> Hi,
> 
> I want to conduct free energy calculations for different orientations of two
> organic molecules to each other. My problem is that I do not find any
> pdb-files for these molecules such as NPB, PTCDA, (dppy)BTPA etc., which are
> used in the area of epitaxial growth. Is there any possibility to create the
> appropriate pdb-file with the correct residue names without a big fuss?
> 

PRODRG, with manual modification of the name after saving the file, or the xleap 
module of AmberTools (which is now free), are two viable options.

-Justin

> Best regards,
> 
> Stefan
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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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