AMBER Archive (2002)

Subject: Re: why are the results so large difference calculating by mm_pbsa and mm_gbsa?

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue Sep 10 2002 - 11:26:07 CDT

Hi,

I'm wondering why the PBCAL line in the ligand column shows 0.00? Are
you sure delphi(?) works in this case? Try commenting the "unlink
$delphiout;" line in the calc_PB routine in mm_pbsa.pl to get delphi log
files.

Best regards

Holger

> I have calculated the free energy with mm_pbsa/gbsa, but the results are very different.
> the system is composed 342 residues protein complexed with a lysine ( with two amino groups,
> one carboxylate, which doesn't exist in amber template, so the charge is fitted by resp method).
> NTV minimization, and NTP molecular dynamics.
>

...

> # COMPLEX RECEPTOR LIGAND
> # ----------------------- ----------------------- -----------------------
> # MEAN STD MEAN STD MEAN STD
> # ======================= ======================= =======================
> ELE -9499.96 57.80 -8993.73 57.50 48.81 1.90
> VDW -1497.10 30.52 -1478.84 30.07 0.66 0.70
> INT 5734.94 46.53 5712.05 46.21 22.89 3.81
> GAS -5262.11 66.63 -4760.51 67.54 72.36 3.78
> PBSUR 85.83 1.05 86.61 1.03 1.05 0.01
> PBCAL -4025.37 23.35 -4060.64 22.85 0.00 0.00
> PBSOL -3939.54 22.97 -3974.02 22.47 1.05 0.01
> PBELE -13525.33 44.88 -13054.37 44.82 48.81 1.90
> PBTOT -9201.65 52.53 -8734.53 53.06 73.42 3.78
> GBSUR 113.89 1.40 114.94 1.37 1.28 0.01
> GB -6226.24 49.28 -6629.58 49.52 -137.64 2.82
> GBSOL -6112.35 48.87 -6514.64 49.13 -136.36 2.82
> GBELE -15726.20 40.88 -15623.31 39.48 -88.83 1.87
> GBTOT -11374.46 44.00 -11275.15 41.98 -64.00 3.27
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -555.04 8.71
> VDW -18.92 3.72
> INT 0.00 0.00
> GAS -573.96 7.15
> PBSUR -1.84 0.07
> PBCAL 35.26 2.01
> PBSOL 33.43 2.00
> PBELE -519.78 7.53
> PBTOT -540.54 6.06
> GBSUR -2.32 0.09
> GB 540.98 6.69
> GBSOL 538.66 6.69
> GBELE -14.06 6.31
> GBTOT -35.30 4.41
>
> Who could give me a hand?
>
> Thanks in advance.
>
>
> 　　　　　　　　　　　　　　Yongjun Jiang
> 　　　　　　　　　　　　　　yjjiang_at_mail.shcnc.ac.cn
> 　　　　　　　　　　　　　　　　　2002-09-10 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++