AMBER Archive (2003)

Subject: AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD

From: Zheng Suxin (sxzheng_at_mail.shcnc.ac.cn)
Date: Thu Nov 06 2003 - 21:41:12 CST

Dear Holger Gohlke,
Thank for your reply. Followed is my calculation example

compound1
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -219.32 5.45
VDW -53.23 2.57
INT 0.00 0.00
GAS -272.55 6.14
PBSUR -3.12 0.19
PBCAL 256.63 6.68
PBSOL 253.51 6.60
PBELE 37.31 4.67
PBTOT -19.05 4.90

compound2
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -210.49 5.40
VDW -52.82 2.35
INT 0.00 0.00
GAS -263.31 5.94
PBSUR -3.37 0.19
PBCAL 248.72 6.63
PBSOL 245.35 6.58
PBELE 38.23 5.38
PBTOT -17.96 5.27

then the result should be :delta deltaG= -1.09; SD= 7.20 (SD^2=SD1^2+SD2^2)

Can we ues mm_pbsa_statistics.pl to calculte two sets data, compound1 and compound2, that is six files such as com1_com.all.out, com1_rec.all.out, com1_lig.all.out, com2_com.all.out, com2_rec.all.out, com2_lig.all.out in the statics.in file, to calculate the delta delta G of each snapshots, and give out the mean delta delta G and the STD. This STD I think would be different from the STD estimated as above approach.

Best Regards

Zheng Suxin

ÔÚ 03-11-6 8:24:00 ÄúдµÀ£º
>Zheng Suxin schrieb:
>>
>> Dear amber,
>> When I use MM_PBSA to calculate the delta G, the program would give a SD(standard deviatia) of the delta G.
>> If I want to get two run's delta delta G, how to estimate the SD.
>
>If you want to combine variances (s_u, s_v) of individual parameters (u,
>v) to get the variance of the result (s_x) and if the fluctuations in
>the observations of u and v are uncorrelated, the following holds:
>
>For x = f(u,v), s_x^2 = s_u^2 * (dx/du)^2 + s_v^2 *(dx/dv)^2.
>
>In the case of DDG = DG2 - DG1, you would get: s_DDG^2 = s_DG2^2 +
>s_DG1^2 for the variance of DDG.
>
>(See e.g. P.R. Bevington, Data Reduction and Error Analysis for the
>Physical Sciences.)
>
>> Can MM_PBSA calculates it automately?
>
>No.
>
>Best regards
>
>Holger
>
>> Thanks
>> sxzheng
>>
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>
>--
>++++++++++++++++++++++++++++++++++++++++++++++++++
>Dr. Holger Gohlke
>
>J.W. Goethe-Universität
>Fachbereich Biologie und Informatik
>Institut für Mikrobiologie
>Marie-Curie-Str. 9
>60439 Frankfurt/Main
>Germany
>
>Tel.: (+49) 69-798-29503; Fax: (+49) 69-798-29826
>Email: gohlke_at_bioinformatik.uni-frankfurt.de
>URL: http://www.rz.uni-frankfurt.de/~hgohlke
>++++++++++++++++++++++++++++++++++++++++++++++++++
>
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>.

                    ÖÂ
Àñ£¡

            Zheng Suxin
            sxzheng_at_mail.shcnc.ac.cn

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