You could use the 'atommap' command in cpptraj to generate a map showing correspondence between atoms in the prep (create a prm/rst based on the prep first) and the pdb. It can also reorder the atoms.
-Dan
On Jun 8, 2012, at 8:35 AM, Chris Whittleston <csw34.cam.ac.uk> wrote:
> 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 - 06:30:03 PDT
