Re: [AMBER] Energy Decomposition using mmpbsa script

From: Eliac Brown <eliacbrown.yahoo.com>
Date: Sat, 12 Mar 2011 07:32:36 -0800 (PST)

Dear Dr. Bill Thanks so much for your reply. First, is mmpbsa.py decomp option working well with amber10? I see on the website, it is mentioned that it is available only with amber11 Secondly, for the difference in the output, I am pretty sure as I believe the input files generated by the different scripts have the same parameters' value: File generated by MMPBSA.py &cntrl    ntb=0, idecomp=0, cut=999.0, nsnb=99999,    imin=5, maxcyc=1, ncyc=0, igb=2,    saltcon=0.150, intdiel=1, extdiel=78.3, gbsa=1,    surften=0.0072, / File generated by mm_pbsa.pl. Using  MM GB MS &cntrl   ntf    = 1,       ntb    = 0,       dielc  = 1.0,   idecomp= 0,   igb    = 2,       saltcon= 0.15,   offset = 0.09,   intdiel= 1.0,     extdiel= 78.3,   gbsa   = 1,       surften= 1.0,   cut    = 999.0,   nsnb   = 99999,   scnb   = 2.0,     scee   = 1.2,   imin   = 1,       maxcyc = 1,       ncyc   = 0, &end The full input and output files are attached Finally, thanks in advance Eliac --- On Sat, 3/12/11, Bill Miller III <brmilleriii.gmail.com> wrote: > From: Bill Miller III <brmilleriii@gmail.com> > Subject: Re: [AMBER] Energy Decomposition using mmpbsa script > To: "AMBER Mailing List" <amber@ambermd.org> > Date: Saturday, March 12, 2011, 1:31 PM > If all the input variables are > exactly the same, then mm_pbsa.pl and > MMPBSA.py should give you the exact same answer for all > components. We made > sure this was the case when we wrote and released > MMPBSA.py. The difference > is that some of the variables have different defaults in > MMPBSA.py than the > suggested values in mm_pbsa.pl, such as igb. > > What are the lines in and surrounding line 358 of > AMBER-10.0/amber10/lib/mm_pbsa/mm_pbsa_readinput.pm ? Also, > could you post > your input file for mm_pbsa.pl? > > And have you tried decomposition analysis with MMPBSA.py? > Did that give you > any problems? > > -Bill > > On Sat, Mar 12, 2011 at 8:05 AM, Eliac Brown <eliacbrown@yahoo.com> > wrote: > > > Dear AMBER > > Firstly, I calculated the mmgbsa binding energy using > mmpbsa.pl and using > > mmpbsa.py, I got the identical final delta energies, > but the the energy > > components for each of ligand, receptor and complex > were different using the > > two mmgbsa scripts, is that normal? (not I used MS=0 > to force the program to > > calculate the solvation using LCPO method as it is > done with pythone > > script). > > Secondly, I am trying to calculate the energy > decomposition using GB model > > (mmpbsa.pl) , if I specified PB = 0 it gives me an > error : > > AMBER-10.0/amber10/lib/mm_pbsa/mm_pbsa_readinput.pm > line 358 > > when I change PB to 1, it works normally, but I don't > need to calculate PB > > where it is very expensive calculation. how can I do > that? > > Thanks in advance for your help > > Eliac > > > > > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER@ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > -- > Bill Miller III > Quantum Theory Project, > University of Florida > Ph.D. Graduate Student > 352-392-6715 > _______________________________________________ > AMBER mailing list > AMBER@ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber >

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Received on Sat Mar 12 2011 - 08:00:02 PST
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