AMBER Archive (2003)

Subject: AMBER: residues and molecules

From: GUILLERMINA L ESTIU (gle10_at_psu.edu)
Date: Tue Sep 23 2003 - 16:56:01 CDT

This is a big question:

I am running amber7. My system is pretty large. It is a trimer of 36600 atoms
(before solvation)
When using tleap everything seems to be fine in building the topology and crd
files. They are running OK with sander
However, the problem appears when trying to run them in parallel, actually when
trying to use pmemd

The problem is that (I don't know how) tleap properly build the residues, but
messes up the definition of the molecules : a molecule ends in the middle of a
residue.
The first molecule ends when finishing chain A, the second when ending chain B.
The second one should end at the end of the chain C, which is also the end of
the first unit (monomer). But it ends 12 atoms further. The error is them
extended to the other units.
I believe that is something related with a unit docked, as in is 12 atom in
length. I have been playing a little changing the position of the unit in the
pdb file, but could not solve the problem.

Does anyone have a hint?
Does leap read in a different way the atom number for residues and for
molecules?

Any opinion is more than welcome!

Guille
Dr Guillermina Estiu
Chemistry Department
Pennsylvania State University
PA 16802

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