Sorry, you are right, the numbers in the masks are atom numbers. I will
try with residue numbers and see if it works.
Em 2014-02-15 09:45, almarques escreveu:
> 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 - 04:00:02 PST
