[AMBER] MMPBSA.py problem

From: Indrajit Deb <biky2004indra.gmail.com>
Date: Thu, 24 Oct 2013 18:01:01 +0530

Dear AMBER users

I am a beginner of AMBER trying to run MMPBSA.py on a set of PDB of a
Protein-DNA complex, which is extracted form a trajectory file. Like single
trajectory method I have generated receptor and ligand pdbs from the
respective complex pdb. Respective prmtop and inpcrd files were generated
using AMBER12 and used for MMPBSA.py as

MMPBSA.py -O -i mmpbsa.in -o RESULTS_MMPBSA$counter0b.dat -do
FINAL_DECOMP_MMPBSA$counter0b.dat -cp comp_mod$counter0b.prmtop -rp
Protein_mod$counter0b.prmtop -lp DNA_mod$counter0b.prmtop -y

where $counter0b is a variable.

My questions are:
1. Whether the method is logical or not?
2. MMPBSA.py giving error if I used 99SBildn or 99bsc0 but work fine for
3. per residue decomposition gives following error:

Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd.1" is missing or

(I have searched the mailing list and I found one suggestion regarding
making change in few line of calculation.py)

looking forward for your kind help

Indrajit Deb
Kolkata, India.
Mob: +919239202278
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Received on Thu Oct 24 2013 - 06:00:03 PDT
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