AMBER Archive (2007)

Subject: AMBER: MM_PBSA calcultion- help me

From: varsha rani (varsha.devil_at_gmail.com)
Date: Tue Oct 16 2007 - 00:53:14 CDT

Dear all,

I am calculating free binding energy for a complex system, having protein
and a small ligand, by using MM_PBSA module in amber9 . As given in the
tutorial, foremost made an input to generate snapshots for three systems,
Complex, Receptor and ligand, from the entire trajectory that i got from
the simulation. The job went fine, as for i know, and it has generated the
snapshots but nothing has been found when i open them.

 Here is the Input:

GENERAL
 PREFIX snapshot
 PATH ../
 COMPLEX 1
 RECEPTOR 1
 LIGAND 1
 COMPT ../_com.top
 RECPT ../_rec.top
 LIGPT ../_lig.top
 GC 1
 AS 0
 DC 0
 MM 0
 GB 0
 PB 0
 MS 0
 NM 0
 @MAKECRD
 BOX YES
 NTOTAL 35000
 NSTART 1
 NSTOP 600
 NFREQ 1
 NUMBER_LIG_GROUPS 1
 LSTART 3256
 LSTOP 3296
 NUMBER_REC_GROUPS 1
 RSTART 1
 RSTOP 3256
 @TRAJECTORY
 TRAJECTORY ../sim1.crd
 TRAJECTORY ../sim2.crd
 TRAJECTORY ../sim3.crd
 @PROGRAMS

 Help me to solve it.

-Live life on your own terms-
Varsha rani

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