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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--
========================================
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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