Dear all:
I have a solvated prmtop file : com_sol.prmtop, and I want calculate MM-PBSA energy, so I use ante-MMPBSA.py to prepare
my prmtop files for ligand, receptor and complex.
First I run:
ante-MMPBSA.py -p com_sol.prmtop -s "!(:1-252)" -c com.prmtop
it successfully generate complex prmtop file: com.prmtop
Next, I should extract receptor and ligand from com.prmtop
I run:
ante-MMPBSA.py -p com.prmtop -m ":1-250" -r rec.prmtop
ante-MMPBSA.py -p com.prmtop -n ":251-252" -l rec.prmtop
error comes:
----------
Error: You specified ligand or receptor mask, but not a ligand and receptor topology file!
---------
I don't know how to do it if I understanding the manual correctly.
Then I run:
ante-MMPBSA.py -p com.prmtop -s ":1-250" -c ligand.prmtop
ante-MMPBSA.py -p com.prmtop -s ":251-252" -c rec.prmtop
all goes well, but I am doubt about weather the ligand.prmtop and rec.prmtop is what I want.
PS: amberTools is version 15
Hope somebody explain it
Thx
Chris
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Received on Tue Jun 16 2015 - 22:00:02 PDT
