[gmx-users] Small organic molecules

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 24 17:41:32 CEST 2009

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.


> Best regards,
> Stefan
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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


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