AMBER Archive (2009)

Subject: Re: [AMBER] pairwise per-residue decomposition

From: manoj singh (mks.amber_at_gmail.com)
Date: Fri Oct 30 2009 - 00:46:22 CDT

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_at_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_at_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_at_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_at_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
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER_at_ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
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> >
> >
>
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