AMBER Archive (2003)

Subject: Re: AMBER: partial charge

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 02 2003 - 00:46:04 CST

On Mon, Dec 01, 2003, Li Ying wrote:
>
> I try use Sander to minimize a 11-mer B-DNA in amber7. When I use XLeap to
> load the pdb file of this duplex, it shows total charge -20. But in output
> file of minimization, it says "Sum of charges from parm topology file =
> -9.9999999".
>
> Why the total charge is not -20 in minimization? Thanks for your help.
>

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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