AMBER Archive (2006)

Subject: Re: AMBER: MM-GBSA decomposition

From: sishi.tang_at_utoronto.ca
Date: Sat Apr 15 2006 - 12:54:34 CDT

Hi Dr. Gohlke,

Here's the *all.out output:
rec.all.out:
MM
GB
MS
1
TDC 117 35.239 -1.484 9.922 -2.399 192.517
TDC 118 24.874 1.229 32.627 -66.840 127.287
TDC 119 20.961 2.108 -104.476 -56.093 245.431
TDC 150 37.665 -0.613 21.247 -7.825 224.365
SDC 117 26.110 -0.615 -4.819 -1.690 142.047
SDC 118 10.155 0.970 33.198 -67.624 111.130
SDC 119 12.379 1.852 -115.395 -58.202 224.328
SDC 150 30.184 -0.307 -5.657 -4.819 146.384
BDC 117 9.129 -0.869 14.741 -0.709 50.470
BDC 118 14.720 0.259 -0.571 0.784 16.156
BDC 119 8.582 0.255 10.918 2.109 21.103
BDC 150 7.481 -0.305 26.904 -3.006 77.981

com.all.out:
MM
GB
MS
1
TDC 117 35.239 -1.484 9.922 -2.396 192.517
TDC 118 24.874 1.229 32.627 -66.830 127.287
TDC 119 20.961 2.108 -104.476 -56.079 245.431
TDC 150 37.665 -0.613 21.247 -7.823 224.365
SDC 117 26.110 -0.615 -4.819 -1.689 142.047
SDC 118 10.155 0.970 33.198 -67.615 111.130
SDC 119 12.379 1.852 -115.395 -58.191 224.328
SDC 150 30.184 -0.307 -5.657 -4.817 146.384
BDC 117 9.129 -0.869 14.741 -0.707 50.470
BDC 118 14.720 0.259 -0.571 0.785 16.156
BDC 119 8.582 0.255 10.918 2.113 21.103
BDC 150 7.481 -0.305 26.904 -3.006 77.981

lig.all.out:
MM
GB
MS
1
TDC 1 89.901 1.316 -58.744 -13.024 521.913
SDC 1 89.901 1.316 -58.744 -13.024 521.913
BDC 1 0.000 0.000 0.000 0.000 0.000

The ligand residue number is 260 in the complex, which is not shown in the
com.all.out file. MM-PBSA works normally if residue 150 is excluded from input.
However, I cannot see any anormaly when residue 150 is concerned in the output
file.
So could you give me some advice on this?

Thanks,
Sishi.

Quoting Holger Gohlke <gohlke_at_bioinformatik.uni-frankfurt.de>:

> Am Donnerstag, 6. April 2006 22:20 schrieb sishi.tang_at_utoronto.ca:
> > Hi all,
> >
> > I'm trying to be MM-GBSA based free energy decomposition. The method
> works
> > in general but fails for one specific residue. An error was given as
> > follows:
> >
> > Argument " Missing BGB for GB in 1+1 (residue 3" isn't numeric in add
> > at /aspirin/software/amber7/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line
> > 1482, <IN> chunk 18.
> > 1)
> >
> > Does anyone have any idea what this means or how to solve it?
>
> Could you have a look at the ...all.out files generated by mm_pbsa.pl? Is
> there any value missing in the BDC sections?
>
> Best regards
>
> Holger
>
> >
> > Thanks,
> > Sishi.
> >
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> --
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> Dr. Holger Gohlke
>
> J.W. Goethe-Universitaet
> Fachbereich Biowissenschaften
> Institut für Zellbiologie und Neurowissenschaft
> Max-von-Laue-Str. 9
> 60438 Frankfurt/Main
> Germany
>
> Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29527
> Email: gohlke_at_bioinformatik.uni-frankfurt.de
> URL: http://www.uni-frankfurt.de/~hgohlke
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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