Yes. For the ligand_mask, :1-3083 corresponds to the protein ligand,
12403 corresponds to the metal, and 12407-12408 corresponds to a water
molecule bound to the metal. Similarly, in the receptor mask I have the
other 3 protein chains + 3 Mn + 3 water molecules.
Do you think the problem is because I have the metal atoms and active
site waters in the end of the pdb file of the complex?
As I said, I prepared the top files for the ligand, receptor and
complex in leap, using the option "default pbradii mbondi2". However, I
didn´t include the mbondi2 in the top file that I used for the
simulation in explicit solvent. Could this also be the problem?
Thank you,
Alexandra
Em 2014-02-14 20:05, Ray Luo, Ph.D. escreveu:
> 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 Sat Feb 15 2014 - 02:00:02 PST
