AMBER Archive (2009)

Subject: RE: [AMBER] compare MMPBSA result

From: Ray Luo (rayhuangluo_at_gmail.com)
Date: Wed Apr 08 2009 - 12:02:41 CDT

For the ligand calculation, please use fillratio=3 or 4 for all of your
snapshots.

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of m m
Sent: Tuesday, April 07, 2009 11:28 PM
To: amber_at_ambermd.org
Subject: [AMBER] compare MMPBSA result

        
    
    
         

        
      

Hi,

i run mmpbsa calculation with amber10, some calcutaion are good but another
calculation stop with this message like:
sander -O -i pbsa_lig.in -o pbsa_lig.155.out -c ./snapshot_lig.crd.155 -p
./mmR18.prmtp not successful.
i solve this problem by adding fillratio=3 to pbsa_lig.in immediately when
he is generated , and the calculation terminate with success.
My question is: Is it correct to compare the calculations where I add
fillratio with those without fillratio,if I had to do?
thanks

    
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