[AMBER] mandatory command lines in MMPBSA.PY

From: Amor San Juan <amorsanjuan.yahoo.com>
Date: Thu, 22 Jul 2010 21:16:25 -0700 (PDT)

Calculation of binding energy has two approaches: 'single trajectory approach' and 'different trajectory approach'. The mmpbsa.pl module can do both. I want to know from the developer of mmpbsa.py if it can also do both.

This is the case of what I want to calculate. My input file does not contain complex, just a standalone ligand, or standalone receptor. Can mmpbsa.py perform calculations if my input file only include a ligand ?

In accord with the manual, there are 6 mandatory command lines for mmpbsa.py which include:

-i input file \
-o output file \
-cp complex_prmtop \
-rp receptor_prmtop \
-lp ligand_prmtop \
-y mdcrd file \

In my case, the only input I have is a ligand, no complex and no receptor. Since abovelisted are mandatory fields, it seems there is no way that mmpbsa.py can calculate for me the binding energy for a ligand alone, or even a receptor alone. I tried several tests but it wasnt successful at all. So before I give up, I want to confirm from developers if this case can not be handled by mmpbsa.py.


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Received on Thu Jul 22 2010 - 21:30:03 PDT
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