Dear AMBER users,
I'm trying to set up a system where NADP+ is the cofactor. I have a PDB
file with initial coordinates for the protein and NADP+, and I have taken
the NADP+ parameters from here (top part, total charge -3):
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/nadp+.prep
I'm absolutely happy putting the complex together using leap, but I'm
currently unable to do so, because I can't figure out which NADP+ atoms in
the PREP file correspond to those in the PDB that I have as the atom names
are different, and I had to add some hydrogens myself. I was hoping to
visualise the PREP file so I could compare it to the PDB that way, but this
doesn't seem possible...
I've looked at the paper which is references for the parameters, but the
authors do not provide any information on atom naming conventions...
Am I missing something obvious?
Many thanks,
Chris
--
*Dr Chris Whittleston*
Department of Chemistry
University of Cambridge
Lensfield Road, Cambridge, CB2 1EW
Email: csw34.cam.ac.uk
Tel: +44 (0)1223 336423
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Received on Fri Jun 08 2012 - 06:00:04 PDT
