AMBER Archive (2005)

Subject: Re: AMBER: MM-PBSA-big energies

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sun Jul 03 2005 - 17:13:48 CDT

when frame 1 is ok and the rest not, I always suspect
1) box info not right (either it expects one and it's missing, or other way
this is easy to check using a text editor

2) wrong prmtop file used (prmtop with water used for stripped
or other way)

since it sounss like you checked this (though I'm not sure exactly
what you're saying about the prmtops, you had 3 of them right?),
you should check the files visually using vmd/moil-view/etc since
it's really easy to pick out problems that way.
good luck
carlos

John wrote:

> Hello,
>
> I have used amber8 for a 10ns MD simulation of a protein with a
> peptide ligand. I am using the MM-PBSA approach to calculate binding
> energies. Prior to that I have used ptraj to strip off the water
> molecules and produce a sample of 3000 frames. I have obtained the
> solvent free trajectory file without box information using the command
> “nobox”. For the MM-PBSA I have also used topology files of the
> protein/peptide alone without the solvent for the receptor, the ligand
> and the complex alike.
>
> Here are some average values after 10ns (from sander):
>
> NSTEP = 1000000 TIME(PS) = 10348.000 TEMP(K) = 299.97 PRESS = 1.0
>
> Etot = -71620.5802 EKtot = 17663.2402 EPtot = -89283.8204
>
> BOND = 471.5498 ANGLE = 1249.2446 DIHED = 1032.0699
>
> 1-4 NB = 570.5820 1-4 EEL = 7585.9984 VDWAALS = 10987.3725
>
> EELEC = -111180.6375 EHBOND = 0.0000 RESTRAINT = 0.0000
>
> EKCMT = 7931.6683 VIRIAL = 7925.6129 VOLUME = 290168.8089
>
> Density = 1.0126
>
> No non-standard residues were used. All initial files were prepared in
> xleap with the ff94 and no error message was given. The overall charge
> of the complex is 0. Also the trajectory viewing did not show any
> obvious glitches, like very close contacts between atoms.
>
> For the MM-PBSA anaylis the standard input file was used as given in
> the examples. Right from the beginning of the calculations I am
> getting big vdw energies:
>
> MM
>
> GB
>
> PB
>
> MS
>
> 1
>
> BOND = 458.3980 ANGLE = 1273.1135 DIHED = 1034.8045
>
> VDWAALS = -1181.8598 EEL = -11779.2769 EGB = -2284.3446
>
> 1-4 VDW = 581.0556 1-4 EEL = 7515.1325 RESTRAINT = 0.0000
>
> corrected reaction field energy: -4753.964000
>
> surface area = 9755.332
>
> 2
>
> BOND = 4523480.6293 ANGLE = 223348.6443 DIHED = 7574.9785
>
> VDWAALS = ************* EEL = -5505.6505 EGB = -2968.0169
>
> 1-4 VDW = ************* 1-4 EEL = 529.2179 RESTRAINT = 0.0000
>
> corrected reaction field energy: -7557.501000
>
> surface area = 10160.164
>
> 3
>
> BOND = 5080825.5589 ANGLE = 211012.6282 DIHED = 7111.4286
>
> VDWAALS = ************* EEL = -4468.8932 EGB = -2793.3557
>
> 1-4 VDW = ************* 1-4 EEL = 1132.4822 RESTRAINT = 0.0000
>
> corrected reaction field energy: -7845.509000
>
> Any suggestion on why Bond, vdw and angle values have exploded would
> be very helpful.
>
> Regards,
>
> John
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor           Phone: (631) 632-1336
Center for Structural Biology Fax:   (631) 632-1555
Stony Brook University        Web:   http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115    E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

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