[AMBER] R.E.D. double bond revisit

From: <psu4.uic.edu>
Date: Wed, 25 Sep 2013 12:51:09 -0500

Dear R.E.D. server,

   If we prepare RESP charges for a molecule with aromatic rings using the
following steps:

   1. Transfer a pdb file into a P2N file. (Scaling factor 1.2, Correct
only redudant atom names , do not modify the atom order, root of the atom
connectivities = 1, 0.0 means a single residue

   2. The generated P2N doesn't seem to include any double bond atom types
/aromatic connectivity from the original pdb file.

   3. The following RESP charge determination using RESP-A1A and
 Gaussian 09 will generate a mol2 file. This mol2 will not have any "ar"
symbol, which represents the C=C bond in a benzyl ring. If we use this
mol2 file to generate .OFF, .frcmod & .prmtop and use acdoctor in
AmberTools to check this generated .prmtop file, it will say "error:
this .prmtop file has an open valance charge at the carbon atoms in the
benzyl ring.

   So from the previous posts
<http://archive.ambermd.org/201202/0246.html> (still
confused after reading the tutorials and the previous posts...so try to
clarify it here....) , it seems like even there is no double bond related
atom type in P2N file, the "aromaticity is still included in RESP charge
calculation. In Xleap, one can simply add double bond/change aromatic
related atom types of benzyl ring in the mol2 file generated from R.E.D.
server, and use this edited mol2 file to generate the .prmtop?

   Hope the post is not too confusing.... If yes, I am more than happy to
re-describe it.

AMBER mailing list
Received on Wed Sep 25 2013 - 11:00:02 PDT
Custom Search