Hi,
I want to use MMPBSA and I gave the following command:
$ MMPBSA.py -O -i mmpbsa.in -o results_mmpbsa.dat -sp 2o3me1c_wat.prmtop -cp
2o3me1c_vac.prmtop -rp 2o3m_vac.prmtop -lp lig_vac.prmtop -y
2o3me1c_md2.mdcrd
It is showing the following:
ptraj found! Using /root/amber11/bin/ptraj
sander found! Using /root/amber9/exe/sander (serial only!)
Assuming /root/amber9/exe/sander is part of
amber9 or amber10. Using old PB input file.
Error: Could not predict mask from topology files! Make sure ligand residues
are
sequential or specify receptor_mask and ligand_mask in the input file.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
(2o3me1c_wat.prmtop = prmtop of solvated complex
2o3me1c_vac.prmtop = prmtop of complex in vacuum
2o3m_vac.prmtop = prmtop of receptor in vacuum,
lig_vac.prmtop = prmtop of ligand in vacuum,
2o3me1c_md2.mdcrd = mdcrd of final production run)
Where am I going wrong?
Kindly help,
Asfa.
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- application/octet-stream attachment: mmpbsa.in
Received on Tue May 25 2010 - 03:30:03 PDT
