AMBER Archive (2009)

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

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Fri Oct 30 2009 - 13:18:52 CDT

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_at_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_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
>> >> > _______________________________________________
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>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >>
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