maria goranovic wrote:
I tried pdb2gmx with an alanine pdb file, with options 5 (opls force
field), 0 (NH3+ n-terminus) and 0 (COO- C-terminus). When I run grompp
on the output from pdb2gmx, I get a total charge of -1.1. Any ideas why
this happens?
The same problem is not there if one looks at a dipeptide. Why the
problem for a single amino acid? It looks like when pdb2gmx applies
patches for the N-terminus and C-terminus to the ends of a protein, it
changes atom types for the peptide backbone. If one uses a single amino
acid, the patches are applied to the same residue, and hence the odd
-1.1 charge? If this is so, is this not a bug?
This is not a bug. You're choosing the wrong termini. With OPLS, there is a
"zwitterion" terminus option that you should be using, since a single amino acid
with two charged termini is a zwitterion.
-Justin
Thank you for inputs,
-maria
--
Maria G.
Technical University of Denmark
Copenhagen
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
