Custom Search
-- 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 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Feb 14 2014 - 12:30:02 PST