Dear Amber user community
I am new amber. I completed my molecular dynamics of protein and liagand complex using NAMD.
After running MD I am intereasted in calculating the binding free energy.
so we have searched and came to know ambers MM/GBPSA method.
Running calculations on normal system...
Beginning GB calculations with /home/amber17/bin/sander
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /home/varun/amber17/bin/sander
calculating complex contribution...
File "/home/amber17/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File "/home/amber17/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/amber17/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/amber17/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /home/amber17/bin/sander failed with prmtop complex.prmtop!
Kindly help to solve this problem.
Regards,Varun Kumar DewakerResearch FellowQSAR & Molecular Modelling LabMPC Division (CSN-202)CSIR- Central Drug Research InstituteLucknow - 226031 (U.P), IndiaMob:+918860194990
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Received on Tue Apr 10 2018 - 08:00:02 PDT
