[AMBER] error in ante-MMPBSA.py

From: Chris <dlutlife223.163.com>
Date: Wed, 17 Jun 2015 12:41:25 +0800 (CST)

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

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Received on Tue Jun 16 2015 - 22:00:02 PDT
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