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 - 09:00:03 PST
