AMBER Archive (2002)

Subject: why is mm_pbsa broken ? (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Mon Aug 26 2002 - 16:50:59 CDT

---------- Forwarded message ----------
Date: Fri, 23 Aug 2002 9:0:30 +0800
From: Yongjun Jiang <yjjiang_at_mail.shcnc.ac.cn>
To: "amber_at_heimdal.compchem.ucsf.edu" <amber_at_heimdal.compchem.ucsf.edu>
Subject: why is mm_pbsa broken ?

Dear all,

I have a question about the perl of mm_pbsa. I use it for free enery calculations following as

the examples in the tutorial. It works very well for calculating the energy of complex (protein

+ ligand), but a "binding" calculation (deltaG for A + B --AB), the program is broken. And

"mm_pbsa.out" is cutoff at the line "calc delta", three files of "com.all.out + rec.all.out+

lig.all.out " exist well, but I couldn't find the important output file " _statistics.out".

the ligand is calculated with antechamber and the force field is used as gaff.dat. by the

way, if I only calculate the energy of ligand, the rate is very very slow, why?

Any suggestions would be greatly appreciated.

Thanks in advance.

Jiang

 
               Yongjun Jiang
               yjjiang_at_mail.shcnc.ac.cn
                                        2002-08-23