Just curious, those numbers in the ligand and receptor masks are
residue numbers?
Ray
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Fri, Feb 14, 2014 at 11:28 AM, almarques <almarques.itqb.unl.pt> wrote:
> 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 - 12:30:02 PST