On Mon, Apr 1, 2013 at 5:42 AM, kureeckal ramesh <
kureeckalramesh.yahoo.co.in> wrote:
> Dear AMBER users
>
>
> Was successful in completing MD simulation for our protein sample. We
> were also able to run successfully the ras-raf tutorial posted on the amber
> web site including the calculation of deltaG
>
> However,
> after generating the snapshots sucessfully, for calculating the binding
> energy for our protein sample , the mm_pbsa.pl perl script is showingan
> error whihc is shown below
>
>
>
> ----------------------------------------------------------------------------------------------------------------------------------------------------
>
> ramesh.sgiUV:~/1FJ1_noheader_info>mm_pbsa.pl binding_energy.mmpbsa >
> binding_energy.log
>
> /data1/apps/amber/10/intel-mkl-openmpi/exe/sander -O -i sander_com.in
> -o sander_com.1.out -c ./snapshot_com.crd.1 -p ./1FJ1_AF.prmtop not
> successful
>
Look in the sander_com.1.out file for the error message.
Another option is to use MMPBSA.py from AmberTools 12, which is a
significantly more up-to-date package then Amber 10.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 01 2013 - 05:30:03 PDT
