Hi,
I have bee trying to run the mmpbsa.py for alanine scanning mutagenesis
but I always get this error:
Loading and checking parameter files for compatibility...
PrmtopError: Couldn't predict mask from topology files!
Your ligand residues must be sequential in your complex.
There are likely problems with your topology files if this is not the
case.
My input is:
sample input file for running alanine scanning
&general
startframe=3000, endframe=5000, interval=1000,
verbose=1,
ligand_mask=':1-200,806,810',
receptor_mask=':201-401,402-603,604-805,807,808,809,811,812,813',
/
&pb
inp=1, radiopt=0, exdi=80, indi=3.0,
cavity_surften=0.00542, cavity_offset=-1.008,
fillratio=4, scale=2.0, linit=1000, istrng=0.100,
/
&alanine_scanning
/
I have four chains, each with a Mn atom and a water molecule bound to
the metal. One of the chains (with its metak and water) is the ligand.
The command that I am using is:
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsaAS2.in -cp com_wt.top -rp
recCFH_wt.top -lp ligB_wt.top -y 10ns_noH2O.mdcrd -mc 2Bcomp.top -ml
2Blig.top -mr recCFH_wt.top &
Am I missing something? Could you help me please?
Thanks,
Alexandra
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Received on Mon Feb 24 2014 - 04:00:02 PST
