AMBER Archive (2008)

Subject: Re: AMBER: something puzzled with mm_pbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Fri Oct 24 2008 - 11:21:59 CDT

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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