AMBER Archive (2003)

Subject: Re: AMBER: partial charge

From: Li Ying (bj_0306_at_yahoo.com)
Date: Tue Dec 02 2003 - 13:19:22 CST

Thanks very much for your reply. Here is my procedure,
After load pdb file of 11-mer B-DNA in xleap, I used the command " saveAmberParm x bdna.top bdna.crd", it shows in xleap "checking unit. WARNING: The unperturbed charge of the unit: -20.00000 is not zero". I generate the pdb file from the prmtop/prmcrd files, the pdb looks fine.
Then I run minimization using my prmtop/prmcrd file:
sander -i min.in -o min.out -p bdna.top -c bdna.crd -r min.res
In mdout file (min.out):
" Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 371 695
| Running AMBER/MPI version on 2 nodes

     Sum of charges from parm topology file = -9.99999994
     Assuming uniform neutralizing plasma "

I get new pdb file from restrt file (min.res). I load this new pdb file and save parm files in xleap, it still has same warning for the unit charge -20.0.
So I wonder why in mdout file of sander sum of charges is not -20 but -9.99?
 

"David A. Case" <case_at_scripps.edu> wrote:

Something is wrong, but there is not enough information here to tell what
it is. When you say "it shows a total charge of -20", can you be more
explicit about exactly what output you are looking at? Look carefully through
your leap.log file to try to find anything that could be changing the charges.
Use ambpdb to generate a pdb file from your prmtop/prmcrd files, and make sure
you still have 20 phosphate groups, etc.

..good luck...dac 

-- 

==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page: 
La Jolla CA 92037 USA | http://www.scripps.edu/case
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