Dear Amber users,
My ligand in protein-ligand complex contains 6 fluorines. I am running MMPBSA calculations with Amber 12 for protein-ligand binding free energy. When I run only MM-PB/GB-SA, it runs fine. But only when I want to decompose energy on per residue basis using &decomp namelist, it crashes with message
bad atom type: f
CalcError: /ibis/bashford/amber12/bin/sander failed with prmtop complex.prmtop!
If I am to suspect complex.prmtop, then it should have given the same error for MM-PB/GB-SA calculations, but it does not.
I did read messages on archive about this same error. Do I need to patch the parameters of Fluorine on Amber 12?
Here are my inputs for
&general
endframe=8000, interval=1000, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1, print_res="2-274; 277-549"
dec_verbose=2,
/
MMPBSA.py -O -i mmpbsa-1.in -o MMPBSA.dat -do MMPBSA_DECOMP.dat -sp complex-tip3.prmtop -cp complex.prmtop -rp DH61-ab.prmtop -lp lig.prmtop -y prod-NVT-8ns.mdcrd prod-NVT-16ns.mdcrd
I am using interval 1000 for test run to make calculation quicker.
Any appreciate help/suggestions.
Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 04 2013 - 11:00:02 PST
