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

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 6 Feb 2012 23:27:13 -0500

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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Received on Mon Feb 06 2012 - 20:30:03 PST