AMBER Archive (2006)

Subject: Re: AMBER: strange mm_pbsa output

From: alfredoq_at_fcq.unc.edu.ar
Date: Sat May 13 2006 - 15:43:53 CDT

Thanks Ray for the hint. The complete mdcrd file and the file with the
stripped
waters were very strange. After loading them in VMD the covalente
structure was
all messed up as you suggested (obviously the snapshots were also
screwed too).
The strange thing is that the structure in the .restrt file is ok. What may
have caused the mdrcrd corruption? The file is quite big (1.5 GB).
Thanks

Alfredo

Quoting Ray Luo <rluo_at_uci.edu>:

> 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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