Em 2014-02-14 19:26, almarques escreveu:
Sorry, I forgot to send the script file in the previous email.
> 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 - 11:30:09 PST
