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$counter0b.prmtop -y
comp_mod$counter0b.inpcrd
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
99SB.
3. per residue decomposition gives following error:
Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd.1" is missing or
unreadable
(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
