Can you attach your topology files here so I can take a look at them?
On Tue, Feb 7, 2012 at 11:25 AM, Shuyi Cao <scao4.uic.edu> wrote:
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 07 2012 - 09:00:02 PST
