AMBER Archive (2008)

Subject: RE: AMBER: something puzzled with mm_pbsa

From: TaoPaul (paultao2008_at_hotmail.com)
Date: Fri Oct 24 2008 - 21:08:50 CDT

 
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 molec!
 ular surface automatically? If it> > can why> > it doesn't shown in th
e 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> >> -----------------------------------------------------------------------> The AMBER Mail Reflector> To post, send mail to amber_at_scripps.edu> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)> to majordomo_at_scripps.edu
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