[AMBER] regarding MMPBSA

From: Asfa Ali <asfa.iisc.gmail.com>
Date: Tue, 25 May 2010 15:45:05 +0530

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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Received on Tue May 25 2010 - 03:30:03 PDT
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