Re: [AMBER] ante-MMPBSA error message:additional OXT atom

From: Shuyi Cao <scao4.uic.edu>
Date: Tue, 7 Feb 2012 10:25:42 -0600

Thank you, Jason.
Actually,I did not use strip_mask to define the ligand. I have tried to
generate my topology files again and again, but still the error message
keeps coming out. I don't know where I did wrong. Everything in VMD and
Chimera look fine. No bond broken or distorted. Could you think of other
ways that may cause the high energy of the bond and Van der Waals?

On Mon, Feb 6, 2012 at 10:27 PM, Jason Swails <jason.swails.gmail.com>wrote:

> This version of ante-MMPBSA was not very flexible or forgiving, so I would
> suggest against trying to use it.
>
> It is much improved for the upcoming release, and will actually be
> generally useful there (instead of just useful for the most common case).
>
> For the time being, I would suggest following the workflow on the net
> tutorials regarding MMPBSA calculations and generating consistent
> topologies yourself.
>
> Also note that the error message you got could be indicative of an
> incompatible strip_mask as well (or a receptor/ligand mask if you provided
> them yourself).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Feb 6, 2012, at 9:03 PM, Shuyi Cao <scao4.uic.edu> wrote:
>
> > Hi all,
> >
> > I want to use MMPBSA to calculate binding energy formy protein conmplex,
> > but my result is very weird, since the van der Waals energy is quite
> high.
> > And an error message showed like this:
> > INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND, ANGLE,
> AND/OR
> > DIHED).
> > CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE
> > RELIABLE (check differences)!
> > The most common cause of this is inconsistent charge definitions across
> > topology files.
> > Complex:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > BOND 7952096.0436 1239353.8273
> > 177050.5468
> > ANGLE 322047.5238 45147.3031
> > 6449.6147
> > DIHED 11885.5386 1351.0769
> > 193.0110
> > VDWAALS 255639253908530208.0000 1262730681757532416.0000
> > 180390097393933216.0000
> >
> >
> > Then I tried to use ante-MMPBSA to generate compatible files for MMPBSA.
> > However, a error message showed like this:
> > Warning: there is an atom OXT in residue ASP237 which does not exist in
> the
> > model ASP!
> > This atom will not be created.
> > residue ASP237 has 13 atoms
> > N
> > H
> > CA
> > HA
> > CB
> > HB2
> > HB3
> > CG
> > OD1
> > OD2
> > C
> > O
> > OXT
> > model ASP has 12 atoms.
> > N
> > H
> > CA
> > HA
> > CB
> > HB2
> > HB3
> > CG
> > OD1
> > OD2
> > C
> > O
> > Warning: cannot find template for residue ASP in our library.
> > You will not be able to save prmtop for this molecule.
> > But ASP 237 is actually the terminal residue of my protein, there must be
> > an additional oxygen atom at the end of this residue. I did not quite get
> > this error message. Could anyone help solve this problem?
> >
> > Thanks in advance for any help!
> >
> > --
> > Shuyi Cao
> > Graduate student
> > Department of Medicinal chemistry and Pharmacognosy
> > College of Pharmacy
> > Univerisity of Illinois at Chicago
> >
> >
> >
> > --
> > Shuyi Cao
> > Graduate student
> > Department of Medicinal chemistry and Pharmacognosy
> > College of Pharmacy
> > Univerisity of Illinois at Chicago
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>
>


-- 
Shuyi Cao
Graduate student
Department of Medicinal chemistry and Pharmacognosy
College of Pharmacy
Univerisity of Illinois at Chicago
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Received on Tue Feb 07 2012 - 08:30:04 PST
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