AMBER Archive (2008)

Subject: RE: AMBER: something puzzled with mm_pbsa

From: Ray Luo (rayhuangluo_at_gmail.com)
Date: Mon Oct 27 2008 - 11:56:54 CDT

Dear Paul,

 

If this is from Amber9, the most likely reason is the inconsistent options
in the input file. Please share with us the input file that is causing the
problem.

All the best,
Ray

 

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

 

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
TaoPaul
Sent: Friday, October 24, 2008 7:09 PM
To: amber_at_scripps.edu
Subject: RE: AMBER: something puzzled with mm_pbsa

 

 
Dear Ray
 
The amber I am using is version 9 obtained by my boss, I am a students of
Key Labortary for Molecular Enzymology and Engineering, the Ministry of
Education, Jilin University in China. Is this you want to know, or something
else?
 
Best wishes!
 
 
> Date: Fri, 24 Oct 2008 09:21:59 -0700
> From: rluo_at_uci.edu
> To: amber_at_scripps.edu
> Subject: Re: AMBER: something puzzled with mm_pbsa
>
> Paul,
>
> Could you be specific which amber distribution you are using?
>
> All the best,
> Ray
>
> On Fri, Oct 24, 2008 at 3:50 AM, TaoPaul <paultao2008_at_hotmail.com> wrote:
> >
> > Hi all
> >
> > when I did practise using mm_pbsa.pl to calculate the free energy of the
> > complex ras-raf
> >
> > provided by amber itself, setting MS=0, PB=1, I found some phenomena
puzzled
> > me!
> >
> > 1.there was not area surface term in the ras_raf_II_wt_com.all.out file,
> > 1
> > BOND = 693.4575 ANGLE = 1895.7111 DIHED! =
> > 1478.8198
> > VDWAALS = -1974.0288 EEL = -17194.5212 HBOND =
> > 0.0000
> > 1-4 VDW = 866.5634 1-4 EEL = 7173.9328 RESTRAINT =
> > 0.0000
> > corrected reaction field energy: -6656.288058
> > ECAVITY = &nbsp! ; 91.5523 EDISPER = 0.0000
> >
> > and in the final log file the following warning existed
> >
> >
> > =>> Reading files
> > Reading ras_raf_II_wt_com.all.out
> > WARNING: Missing SURF for MS in 0 -> Taken from -1
> > WARNING: Missing SURF for MS in 1 -> Taken from 0
> > WARNING: Missing SURF for MS in 2 -> Taken from 1
> > WARNING: Missing SURF for MS in 3 -> Taken from 2
> >
> > although the situation mentioned above existed, the
> > ras_raf_II_wt_statistics.out file
> >
> > could still be obtained.
> > # MEAN STD
> > # ======! =================
> > ELE ! -9997.78 32.24
> > VDW - 1109.05 8.26
> > INT 4062.38 24.18
> > GAS -7044.46 34.03
> > PBSUR 91.55 0.13
> > PBCAL -4003.86 31.15
> > PBSOL -3912.32 31.17
> > PBELE -14001.65 31.14
> > PBTOT -10956.78 20.92
> >
> > However, when you set MS=1 or (MS=0, GB=1), the area surface both
existed !
> > in the
> >
> > ras_raf_II_wt_com.all.out file.
> >
> > 2. when you tried to calculate the binding free energy, setting MS=0
PB=1
> > the procedure
> >
> > stopped at
> > "=>> Calc delta from raw data
> > No data for 0+0 MS SURF 0 "
> >
> > Now my questions are following:
> > 1.Can the PBSA procedure generate the molecular surface automatically?
If it
> > can why
> > it doesn't shown in the ras_raf_II_wt_com.all.out file and give the
warning
> > mentioned above
> >
> >! ; and interrupted the binding energy calculation, if not how does the
value of
> > PBSUR in the
> >
> > ras_raf_II_wt_statistics.out get?
> >
> > 2.what should I do if I want to calculate the binding free energy with
MS=0
> > PB=1. I have to
> >
> > do it because my system studying have F elements while I don't know the
> > radius parameter.
> >
> > Best wishes!
> >
> > Paul Tao
> >
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  _____

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