Hi, Ray,
I have several questions. Could you give me some ideas?
Do I have to use DelPhi to calculate polar solvation energy? If I use the PB
program in Amber8, what radii are used? I read Holger's paper, it seems that
the results of the PB method depends on radii. If I set IGB 2, do I need to
use "Pbradii mbondi2" when I generate top files?
Thank you!
Wei
Quoting Ray Luo <rluo.uci.edu>:
> Okay, could you email me your output and log files for your mmpbsa script?
>
> Best,
> Ray
>
> Wei Chen wrote:
>
> >Hi Ray,
> >
> >I didn't use Delphi. I used pb program in Amber8. I find a problem. I check
> the
> >
> >values of "corrected reaction filed energy". Its mean is not equal to
> >the "PBCAL". Why is that?
> >
> >Thank you!
> >
> >Wei
> >
> >ÒýÓÃ Ray Luo <rluo.uci.edu>:
> >
> >
> >
> >>Hi Wei,
> >>
> >>Could you email me your files so I can take a look why your pbsa output
> >>disagrees with your Delphi output? Please email me the files only for
> >>the snapshot where you see the largest difference.
> >>
> >>Best,
> >>Ray
> >>
> >>Wei Chen wrote:
> >>
> >>
> >>
> >>>Hi, Ray,
> >>>
> >>>Thank you for your reply!
> >>>
> >>>Did you mean bugfix.49? It supposed to be fix by my administor. But I
> >>>
> >>>
> >>checked
> >>
> >>
> >>>the pb_force.f file. It doesn't. I am wondering how I can "temporarily
> >>>
> >>>
> >>force
> >>
> >>
> >>>the net charges of neutral systems zero within rounding error". Actually,
> >>>
> >>>
> >>my
> >>
> >>
> >>>proteins have a net charge '+1'.
> >>>
> >>>The radii for pb and gb are used as the same as those in the "Example"
> >>>
> >>>
> >>fold.
> >>
> >>
> >>>Regards,
> >>>
> >>>Wei Chen
> >>>
> >>>
> >>>Quoting Ray Luo <rluo.uci.edu>:
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>Did you patch bugfix.48 for pbsa? Are you sure you have used the same
> >>>>radii for pb and gb?
> >>>>
> >>>>Wei Chen wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>Hello, all Amber users,
> >>>>>
> >>>>>I am using mm_pbsa in Amber8 to calculate binding free energy of
> >>>>>
> >>>>>
> >>two-protein
> >>
> >>
> >>>>>binding. When I used PB or GB to calculate polar solvation energy, I got
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>very
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>different values. The free energies (not including entropy) are
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>93.28+/-90.46
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>kcal/mol with PB and -37.43+/-5.54 kcal/mol with GB. First of all, the
> >>>>>
> >>>>>
> >>mean
> >>
> >>
> >>>>>value with PB is positive, which doesn't make any sense. And the
> standard
> >>>>>deviation with PB is so large that it is the same order as the mean
> >>>>>
> >>>>>
> >>value.
> >>
> >>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>The
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>value with GB seems to be more acceptable. However, I think that GB is
> an
> >>>>>approximation to PB. So anybody can help me to understand the results?
> >>>>>
> >>>>>Thanks!
> >>>>>
> >>>>>Wei Chen
> >>>>>
> >>>>>--
> >>>>>
> >>>>>-----------------------------------------------------------------------
> >>>>>The AMBER Mail Reflector
> >>>>>To post, send mail to amber.scripps.edu
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> >>>>>
> >>>>>.
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>--
> >>>>====================================================
> >>>>Ray Luo, Ph.D.
> >>>>Department of Molecular Biology and Biochemistry
> >>>>University of California, Irvine, CA 92697-3900
> >>>>Office: (949)824-9528 Lab: (949)824-9562
> >>>>Fax: (949)824-8551 e-mail: rluo.uci.edu
> >>>>Home page: http://rayl0.bio.uci.edu/rayl/
> >>>>====================================================
> >>>>
> >>>>-----------------------------------------------------------------------
> >>>>The AMBER Mail Reflector
> >>>>To post, send mail to amber.scripps.edu
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> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>--
> >>>
> >>>-----------------------------------------------------------------------
> >>>The AMBER Mail Reflector
> >>>To post, send mail to amber.scripps.edu
> >>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >>>
> >>>.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>--
> >>====================================================
> >>Ray Luo, Ph.D.
> >>Department of Molecular Biology and Biochemistry
> >>University of California, Irvine, CA 92697-3900
> >>Office: (949)824-9528 Lab: (949)824-9562
> >>Fax: (949)824-8551 e-mail: rluo.uci.edu
> >>Home page: http://rayl0.bio.uci.edu/rayl/
> >>====================================================
> >>
> >>-----------------------------------------------------------------------
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> >>
> >>
> >>
> >
> >
> >
> >
>
> --
> ====================================================
> Ray Luo, Ph.D.
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
> Office: (949)824-9528 Lab: (949)824-9562
> Fax: (949)824-8551 e-mail: rluo.uci.edu
> Home page: http://rayl0.bio.uci.edu/rayl/
> ====================================================
>
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>
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Received on Mon Nov 14 2005 - 22:53:01 PST
