AMBER Archive (2006)

Subject: Re: AMBER: strange mm_pbsa output

From: Ray Luo (rluo_at_uci.edu)
Date: Fri May 12 2006 - 19:22:57 CDT

It seems that your covalent terms are all screwed up. It is likely that
your water-free snapshots are inconsistent with your water-free prmtop
files. To confirm this, you can try to visualize these files in VMD. If
they mismatch, you wouldn't be able to see correct structures.

alfredoq_at_fcq.unc.edu.ar wrote:

>Dear Amber community,
>
>I applyed the mm_pbsa.pl script to determine the binding free energy o a ligand
>to a protein. My statistics.out file shows the following:
>
># COMPLEX RECEPTOR LIGAND
># ----------------------- -----------------------
>-----------------------
># MEAN STD MEAN STD MEAN
>STD
># ======================= =======================
>=======================
>ELE -5303.15 5519.36 -5155.80 5535.87 -136.49
>54.45
>VDW -2632.54 0.00 -2602.06 0.00 3789742.36
>12298842.54
>INT 49573990.99 8657606.35 49456164.03 8679472.59 117868.77
>287132.38
>GAS 49566055.30 8658148.78 49448406.17 8679936.88 3907474.64
>12302734.61
>PBSUR 169.35 8.90 169.16 8.64 2.75
>0.29
>PBCAL -15530.45 2187.51 -15500.38 2171.48 -65.88
>23.29
>PBSOL -15361.11 2187.01 -15331.21 2171.10 -63.13
>23.22
>PBELE -20833.60 5366.67 -20656.18 5341.50 -202.37
>54.81
>PBTOT 49550694.19 8657701.57 49433074.95 8679489.35 3907411.51
>12302734.03
>GBSUR 243.86 12.82 243.60 12.44 3.96
>0.41
>GB -17701.21 1411.59 -17683.36 1406.15 -69.60
>26.15
>GBSOL -17457.35 1405.56 -17439.76 1400.41 -65.64
>26.06
>GBELE -23004.36 5678.48 -22839.16 5681.10 -206.09
>55.32
>GBTOT 49548597.95 8657432.67 49430966.41 8679215.96 3907408.99
>12302735.31
>
># DELTA
># -----------------------
># MEAN STD
># =======================
>ELE -10.86 79.84
>VDW -3789772.84 12298842.54
>INT -41.81 373.08
>GAS -3789825.50 12298813.02
>PBSUR -2.57 0.78
>PBCAL 35.80 213.86
>PBSOL 33.24 213.81
>PBELE 24.95 222.28
>PBTOT -3789792.27 12298821.27
>GBSUR -3.70 1.12
>GB 51.75 50.11
>GBSOL 48.06 49.49
>GBELE 40.90 78.04
>GBTOT -3789777.45 12298812.93
>
>Analyzing these results I was very stranged by the quite large values of the VDW
>and GAS components and the corresponding SD. During the calculation the
>following warning messages appeared:
>
>vertex atom mismatch
> atom: 1398
>vertex atom: 1395
>molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.
>vertex atom mismatch
> atom: 2429
>vertex atom: 2428
>vertex atom mismatch
> atom: 2798
>vertex atom: 2795
>vertex atom mismatch
> atom: 2998
>vertex atom: 2995
>vertex atom mismatch
> atom: 3098
>vertex atom: 3095
>No skew or curtosis when zero variance in moment
>No skew or curtosis when zero variance in moment
>No skew or curtosis when zero variance in moment
>No skew or curtosis when zero variance in moment
>No skew or curtosis when zero variance in moment
>No skew or curtosis when zero variance in moment
>
>I run the MD simulation in explicit solvent, and I stripped the waters and
>counter ion previous to the mm_pbsa analysis. I also created new prmtop files
>of the complex, the receptor and ligand without waters for mm_pbsa.
>Any hint about what's going wrong with my system or why these large values
>appears would be greatly appreciated,
>Thanks
>
>Alfredo Quevedo
>Facultad de Ciencias Químicas
>Universidad Nacional de Córdoba
>Argentina
>
>
>
> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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