AMBER Archive (2009)

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

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Fri Oct 30 2009 - 00:15:40 CDT

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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