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.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.bioinformatik.uni-frankfurt.de
URL: http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
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Received on Mon Apr 26 2004 - 14:53:00 PDT
