Dear Scott,
Thank for your kind reply. I do as u suggested. i have a doubt..
Along with the empty snapshot files MM_PBSA generated three additional
files with the names (fort.10, fort.11, and fort.12) which are having the
last set of coordinates for Commplex, Receptor and Ligand respectively. I
would like to know What are those files? Is there any bug in MM_PBSA?
-Live life on your own terms-
Varsha
On 10/16/07, Scott Pendley <scott.pendley.gmail.com> wrote:
>
> 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.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 3257
> > 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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Received on Sun Oct 21 2007 - 06:07:03 PDT
