AMBER Archive (2007)

Subject: Re: AMBER: MM_PBSA calcultion- help me

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Tue Oct 16 2007 - 12:24:34 CDT

Varsha,

I would look carefully at all files in the execution or path directory.
Occasionally errors can be found in the output files of the individual
programs that MM-PBSA calls.

Scott

On 10/15/07, varsha rani <varsha.devil_at_gmail.com> wrote:
>
> 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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