Hi,
I ran a MD simulation (in amber 9) of a protein containing 4 subunits,
each with a Mn atom bound to 4 amino acids (modelled as non-standard
residues). Now I want to perform alanine scanning mutagenesis and I want
to use the PB method. I tried the old mm-pbsa script but I had the
problem with the Mn radius. So, I followed the recommendations of the
amber archive: I used the mm-pbsa script implemented in amber 12 with
inp=1 and radiopt=0 (the top files contain the bondii radii); I am
sending the script in attachment. However I had the following error:
Can't use an undefined value as an ARRAY reference at
/opt/programs/amber/12/gnu-4.4.5//src/mm_pbsa/mm_pbsa_statistics.pm line
956.
Then, I tried to use the mmpbsa.py with the following input:
sample input file for running alanine scanning
&general
startframe=3000, endframe=5000, interval=1000,
verbose=1,
ligand_mask=":1-3083,12403,12407-12408",
receptor_mask=":3084-12402,12404-12406,12409-12410,12411-12414",
/
&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
/
However I got the following 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.
Since, I used the mask option I don't understand the reason for this
error. In the complex file I have the 4 metal atoms and 4 water
molecules after the 4 protein chains, like this:
chain A
TER
Chain B
...
TER
Mn A
TER
Mn B
...
WAT A
...
END
Could this be the source of the error? Could someone please give me
some advice about the best way to perform the alanine scanning
mutagenesis (the mm-pbsa.pl or the mm-pbsa.py) for this protein,
considering that it contains 4 chains with Mn atoms?
Thanks in advance
Alexandra
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Received on Fri Feb 14 2014 - 11:30:08 PST
