Dear Chris,
If you look in the F-90 project in R.E.DD.B. you can find NADP+ and
derivatives; more than 200 cofactors generated from a highly
consistent approach...
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
the FF libraries are provided in the mol2 file format and more easy
displayable in graphical programs.
you just run: tleap -f script1.ff
(after having read/modified this script according to the file names)
regards, Francois
> 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
>
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Received on Fri Jun 08 2012 - 07:30:03 PDT
