Dear Dr. Chris Moth;
Thank you very much for your very quick response to my question.
According to your indication, I copied all the snapshot files of the
Examples to my 03_MMPBSA_Binding directory. Taking all complex, receptor and
ligand, and PB=1 this time, quite the same results as in the Examples
ras_raf_II_wt_comall.out and ras_raf_II_wt_statics.out have been obtained.
I should have read the Examples more carefully and understood them.
Thank you again.
Kazuo Koyano
Center for Collaborative Research, The University of Tokyo
4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, JAPAN
Tel; 03-5452-6587 Fax; 03-5452-6545
E-mail koyano.fsis.iis.u-tokyo.ac.jp
----- Original Message -----
From: "Chris Moth" <chris.moth.vanderbilt.edu>
To: <amber.scripps.edu>; "Gohlke Holger" <gohlke.scripps.edu>
Cc: <koyano.fsis.iis.u-tokyo.ac.jp>
Sent: Friday, September 26, 2003 12:56 AM
Subject: AMBER: MM_PBSA(GBSA) Examples
> Hi Kazuo:
>
> When I tried to open your mm_pbsa_2.in attachment, it contained
> a lot of extraneous ASCII - font directives and so forth. Perhaps that
> is part of the problem.
>
> Your attachment's PREFIX line refers to snapshot files that are not
supplied
> in the Example directories on our Amber 7 distribution here.
>
> So, starting from the mm_pbsa.in file in my 03_MMBPSA_Binding directory, I
> created a ligand-only input file with PB=0 to try to duplicate your
errors:
>
> .GENERAL
> PREFIX ras_raf_II_wt
> PATH ../01_GenerateSnapshots/
> COMPLEX 0
> RECEPTOR 0
> LIGAND 1
> COMPT ../ras_raf_II_wt.prmtop
> RECPT ../ras_II_wt.prmtop
> LIGPT ../raf_wt.prmtop
> GC 0
> AS 0
> DC 0
> MM 1
> GB 1
> PB 0
> MS 1
> NM 0
> .GB
> IGB 4
> SALTCON 0.00
> EXTDIEL 80.0
> SURFTEN 0.0072
> SURFOFF 0.00
>
> Running mm_pbsa with the above as the input file, from the
03_MMBPSA_Binding
> directory gives me this statistics file at the end:
>
> # MEAN STD
> # =======================
> ELE -2041.95 13.35
> VDW -290.72 7.24
> INT 1273.52 24.76
> GAS -1059.15 22.28
> GBSUR 31.38 0.12
> GB -1638.92 10.98
> GBSOL -1607.55 10.98
> GBELE -3680.88 10.73
> GBTOT -2666.69 22.79
>
> I hope some of this is helpful. I am learning MM_PBSA myself - and look
> forward to hearing the final solution.
>
> Cheers
>
> Chris
>
> >===== Original Message From amber.scripps.edu =====
> >Dear Dr. Holger Gohlke and Amber users;
> >
> > I have tried to run MM_PBSA(GBSA) Examples 03_MM_PBSA_Binding.
> >Selecting only ligand and GB for the first time, I made the input file as
> >attached.
> >Run the mm_pbsa.pl, the log file stopped at the => Treat Special
Parameters,
> >saying "Can't use an undefined value as an Array reference at
> >/usr/local/amber7/src/mm_pbsa/_statics.pm line 1234.
> >I referred to AMBER Archive to find no suggestion.
> >I would appreiciate it very much if you kindly tell me the solution.
> >Sincerely Yours.
> >Kazuo Koyano
> >
> >Center for Collaborative Research, The University of Tokyo
> >4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, JAPAN
> >Tel; 03-5452-6587 Fax; 03-5452-6545
> >E-mail koyano.fsis.iis.u-tokyo.ac.jp
>
> Chris Moth
> chris.moth.vanderbilt.edu
>
>
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Received on Fri Sep 26 2003 - 11:53:02 PDT
