Could you take a look of the PBSA output file to see what's the error
message?
Ray Luo, Ph.D.
On Feb 13, 2010, at 8:49 AM, Jagdeesh C <jagc666.gmail.com> wrote:
> Dear Amber Users,
>
> I am presently following the MM PBSA tutorials
> http://ambermd.org/tutorials/advanced/tutorial3/section2.htm
>
> I collected 600 snapshots from my production run and used the
> binding_energy.mmpbsa script file to evaluate the binding energy
> http://ambermd.org/tutorials/advanced/tutorial3/section3.htm
>
> When i submitted the following command
> ./mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>
> I got this error
> /root/AMBERTOOLS/amber10/exe/sander -O -i pbsa_lig.in -o pbsa_lig.
> 51.out -c
> /root/AMBERTOOLS/amber10/exe/jag_H3new/testsnapshot_lig.crd.51 -p
> ./njlig_h3.prmtop not successful
>
> I am unable to figure out why this is happening. When I use vmd to
> visualize
> just the ligand (51'st snapshot) it looks perfectly fine. How can I
> overcome
> this problem and what problem is it exactly?
>
> Many Thanks,
> Jagdeesh
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Received on Sat Feb 13 2010 - 10:00:02 PST
