Subject: A question about the RTF and Param. data in CHARMM for my ligand HPO4(2-)!

From: Joe Huang <[email-masked]>
Date: Wed, 15 Dec 1999 11:59:53 -0600

Dear CCLers:

I am trying to do the MD simulations with CHARMM for my protein (PBP:
phosphate binding protein) with ligand HPO4 (2-) positioned close to the
binding pocket.
I put my ligand into another segment for CHARMM to read and I am not
sure if
CHARMM has information for HPO4 (2-) in the RTF and Parameter files!
Actually
I could not find the informations for HPO4(2-) in those files!

I still did the test run and view the resulting  CHARMM DCD files with
VMD program.  In the beginning stages, the whole box with solvent,
protein, xtal waters, and ligand (I have 4 segments identified as
SOLV, SOLU, XWAT, and HPO4 for CHARMM) looks all right, but in the later

stages, the HPO4(2-) ligand was distorted and not in the right
conformation although
it's moving around; some bonds in the ligand became enormously long and
the
angles or dihedrals were totally wrong in the ligand!

Can somebody give me some ideas to solve these problems and where can I
find the
right parameters or rtf data for HPO4 (2-)?
I will compile and organize the responses to give everybody once I solve
the problems!
Thanks!

Merry Christmas and Happy New Year!

Joe, :-)

BCHS, UH
[email-masked]