Thanks for the reply.
I think problem was something else.
In the sander output, there are five terms; internal, vdw, eel, Gpol, ans
sas. I think sas is the solvent accessible surface are which need to
multiply by 0.0072 to get the Gsa.
Am I right?
I will be very thankful for the reply.
Manoj
On Fri, Oct 30, 2009 at 2:18 PM, Tom Joseph <ttjoseph.gmail.com> wrote:
> That is possible...presumably the other residues cancel out its
> effect. Also, did you average over a number of frames?
>
> --Tom
>
> 2009/10/30 manoj singh <mks.amber.gmail.com>:
> > Thanks for your reply.
> >
> > I got this part working.
> >
> > Now, I want to calculated the contribution of the residue towards ligand
> > binding affinity( the ligand is a peptide). I am adding binding affinity
> > contribution of that residue of protein with all residues of the ligand.
> > However, the number I am getting is higher than the total MM-GBSA binding
> > affinity of the ligand.
> >
> > I will be very thankful for any suggestion.
> >
> > Sincerely,
> > Manoj
> >
> > On Fri, Oct 30, 2009 at 1:15 AM, Tom Joseph <ttjoseph.gmail.com> wrote:
> >
> >> To get an energy decomposition, run sander with imin=1 and idecomp set
> >> to the type of analysis you want (in this case 4). Run with no
> >> periodic boundary conditions (ntb=0) and an "infinite" cutoff
> >> (cut=999). See below for an example mdin file that does an MM/GBSA
> >> calculation on a 709-residue structure. It will generate a huge mdout
> >> file which you can then postprocess manually as you wish. Please be
> >> sure to check the values of the parameters to be sure they are what
> >> you really want before using them.
> >>
> >> --Tom
> >>
> >> complex.crd.1 (MM)
> >> &cntrl
> >> cut = 999.0,
> >> dielc = 1.0,
> >> extdiel = 80.0,
> >> gbsa = 2,
> >> idecomp = 4,
> >> igb = 2,
> >> imin = 1,
> >> intdiel = 1.0,
> >> maxcyc = 1,
> >> ncyc = 0,
> >> nsnb = 99999,
> >> ntb = 0,
> >> ntf = 1,
> >> offset = 0.09,
> >> saltcon = 0.0,
> >> scee = 1.2,
> >> scnb = 2.0,
> >> surften = 0.0072,
> >> &end
> >> Residues for decomposition
> >> LRES 1 709
> >> END
> >> Residues to print
> >> RES 1 709
> >> END
> >> END
> >>
> >>
> >> 2009/10/29 manoj singh <mks.amber.gmail.com>:
> >> > Thanks for your reply!
> >> > I relatively new to Amber and therefore not very experienced in doing
> >> these
> >> > type of calculations. I will be very thankful if you can please tell
> me
> >> how
> >> > exactly did yo perform this calculation without using mm_pbsa.pl. I
> am
> >> > trying to do this calculation for last 3 weeks but has not
> >> been successful.
> >> > I will be very thankful for your kind reply.
> >> > Sincerely,
> >> > Manoj
> >> > On Thu, Oct 29, 2009 at 8:30 PM, Tom Joseph <ttjoseph.gmail.com>
> wrote:
> >> >>
> >> >> I had the same problem with this script for ~1000 frames of my ~700
> >> >> residue system on a machine with 8GB of RAM. It would just sit there.
> >> >> I don't know what the problem is, but I gave up on it and now just
> run
> >> >> sander manually and postprocess its output outside of MM_PBSA.pl.
> >> >>
> >> >> You can try running "top" in another terminal session on the same
> >> >> machine while your 1000-frame calculation is attempting to run to get
> >> >> an idea of its memory usage. Look at the "RES", "RSS", or similar
> >> >> column.
> >> >>
> >> >> --Tom
> >> >>
> >> >> 2009/10/29 manoj singh <mks.amber.gmail.com>:
> >> >> > Hi all,
> >> >> >
> >> >> > I am trying to do pairwise per-residue decomposition of MM-GBSA
> >> binding
> >> >> > free
> >> >> > energy for a protein ligand system. My calculation is crashing (the
> >> >> > computer
> >> >> > stop responding) on the "=>> Calc delta from raw data", probably
> due
> >> to
> >> >> > the
> >> >> > memory issue. I will be very thankful if some one can tell me a fix
> of
> >> >> > this
> >> >> > problem.
> >> >> >
> >> >> > Manoj
> >> >> > _______________________________________________
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> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >>
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> >> >
> >> >
> >>
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Received on Fri Oct 30 2009 - 11:30:03 PDT
