AMBER Archive (2004)

Subject: Re: AMBER: mm_pbsa examples; delphi in mm_pbsa

From: Kazuo Koyano (koyano_at_fsis.iis.u-tokyo.ac.jp)
Date: Fri May 14 2004 - 04:35:36 CDT

Dear Dr. Holger;

 Thank you very much for your mail.
It was found after all that delphi itself was not a normal one. I
re-downloaded delphi and have tested the example 02_MMPBSA_Stability to get
almost the same results as save file except very small numerical values.The
cause was not due to the difference of version 2nd and 4th.
I am sorry to have troubled you so much.
Sincerely Yours.

Kazuo Koyano

Center for Collaborative Research, The University of Tokyo
4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, JAPAN
E-mail koyano_at_fsis.iis.u-tokyo.ac.jp

 ----- Original Message -----
 From: "Holger Gohlke" <gohlke_at_bioinformatik.uni-frankfurt.de>
 To: <amber_at_scripps.edu>
 Sent: Monday, April 26, 2004 10:11 PM
 Subject: Re: AMBER: mm_pbsa examples; delphi in mm_pbsa

> Kazuo Koyano schrieb:
> >
> > Dear AMBER developers and users,
> >
> > I have tried mm_pbsa examples. It seems that PB doesn't work properly
> > from an example 02_MMPBSA_Stability as seen below.
> > In the statics.out file, PBCAL= 0 compared to the large value of the
> > save file. In the log file, a line of 'Entry 0 PB PB 0 exists ->
overwriting'
> > of the save file is not found. What are the cause of these?
> > My circumstances are; Amber7, Red Hat Linux Ver.7.3, DelPhi Ver.4.0,
> > delphi was not compiled but installed executables.
>
> The mm_pbsa script has been tested with Delphi II, not Delphi Version
> 4.0, so there might be differences in the output of delphi. If you
> comment the line "unlink $delphiout;" in the function calc_delphi in the
> file mm_pbsa_calceneent.pm, you should get an output file from delphi.
>
> If you send me this output file, I will have a look as to what has
> changed.
>
> Best regards
>
> Holger
>
> >
> > ras_raf_II_wt_statics.out
> > # MEAN STD
> > # =======================
> > ELE -9997.78 32.24
> > VDW -1109.05 8.26
> > INT 4062.38 24.18
> > GAS -7044.46 34.03
> > PBSUR 61.87 0.30
> > PBCAL 0.00 0.00
> > PBSOL 61.87 0.30
> > PBELE -9997.78 32.24
> > PBTOT -6982.59 34.12
> > GBSUR 82.06 0.40
> > GB -2794.51 18.64
> > GBSOL -2712.45 18.51
> > GBELE -12792.30 25.07
> > GBTOT -9756.91 19.97
> >
> > mm_pbsa.log
> > .........................................
> > =>> Reordering files
> > Final order:
> > 1. ras_raf_II_wt_com.all.out: -
> > =>> Reading files
> > Reading ras_raf_II_wt_com.all.out
> > =>> Treat special parameters
> > =>> Calc missing parameters
> > ............................................
> >
> > Thanks in advance
> >
> > Kazuo Koyano
> >
> > Center for Collaborative Research, The University of Tokyo
> > 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, JAPAN
> > E-mail koyano_at_fsis.iis.u-tokyo.ac.jp
> >
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> --
> !!! Please note new telephone number !!!
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> Dr. Holger Gohlke
>
> J.W. Goethe-Universität
> Fachbereich Biologie und Informatik
> Institut für Mikrobiologie
> Marie-Curie-Str. 9
> 60439 Frankfurt/Main
> Germany
>
> Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29826
> Email: gohlke_at_bioinformatik.uni-frankfurt.de
> URL: http://www.rz.uni-frankfurt.de/~hgohlke
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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>

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