AMBER Archive (2003)

Subject: Re: MM_PBSA (Amber7) and delphi

From: CUI, Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Fri Mar 21 2003 - 09:04:04 CST

Hi,
    I'm not sure if they're recommended ones, but you can print out
    charges and radii from ptraj with dumpq and parse in trajout. That'll
    dump amber partial charges and parse radii.

On Fri, 21 Mar 2003, Sue Heavner wrote:

> Hi Amber Users,
> Is anyone using delphi and mm_pbsa in Amber 7 for calculations on DNAs?
> If so what charge and radii files are you using? The examples in
> MM_pbsa using delphi and in delphi itself run fine (they are all
> calculations on proteins) but when I run my files I get an output of 0
> for PBCAL. I am using the academic version (delphi II) from Barry
> Honig's group, not the Insight-delphi version. Thanks in advance for
> your help. Sue
>
> 

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790