Thank you for your reply.
Actually, there is a TER card at the end of protein to separate protein and
ligand. Then, I am just wondering how this error message came out.
On Mon, Feb 6, 2012 at 8:35 PM, liu junjun <ljjlp03.gmail.com> wrote:
> You need manually add a new line of "TER" under the line containing "OXT"
> in your PDB file to separate the protein and ligand (or whatever after the
> protein in PDB file) .
>
> Junjun
>
> On Tue, Feb 7, 2012 at 10:03 AM, 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
> > _______________________________________________
> > AMBER mailing list
> > 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 Mon Feb 06 2012 - 19:00:03 PST
