Hello,
All that parmchk does is search through the specified parameter file and
matches the parameters it finds, including wildcards. Furthermore, the
dihedral parameter in question is an improper, so it's not formed as a
sequence between 2 atoms separated by 3 consecutive bonds. The dihedral I
think it's finding is
X -X -CW-H4 1.1 180. 2.
located in parm10.dat. This is an improper formed from these 2 atoms and 2
other atoms (X is a wildcard). I'm not exactly sure why it's printing it in
the frcmod with CW-H4 in the middle, but it's the same dihedral, I'm pretty
sure. This dihedral is also in parm99.dat, so you should get the same
result dihedral using parm99.dat instead.
Hope this helps,
Jason
On Wed, Sep 29, 2010 at 7:50 AM, Alan <alanwilter.gmail.com> wrote:
> Dear Case and Jason,
>
> Thanks a lot for your observations.
>
> It is much clearer now for me. I am sticking with ff99SB.
>
> However, I still see an issue with dihedral CG-HD2-CD2-NE2 (CC-H4-CW-NA in
> HHH_AC.frcmod). So, it is indeed not Antechamber which is generating the
> dihedrals, it "parmchk".
>
> The atom types in HHH_gas_amber.mol2 are correct as they matched
> identically
> those from reference.
>
> Then, I did another test, based on Case1, by manually removing the dihedral
> I believe is wrong from HHH_AC.frcmod:
>
> IMPROPER
> H5-NA-CR-NB 1.1 180.0 2.0 General
> improper
> torsional angle (2 general atom types)
> CR-CW-NA-H 1.0 180.0 2.0 General
> improper
> torsional angle (2 general atom types)
> ------> removed! CC-H4-CW-NA 1.1 180.0 2.0
> General improper torsional angle (2 general atom types)
> CT-N -C -O 10.5 180.0 2.0 General
> improper
> torsional angle (2 general atom types)
> CT-O2-C -O2 10.5 180.0 2.0 General
> improper
> torsional angle (1 general atom type)
>
> And got, correctly, DIHED = 17.9163, matching the reference value.
>
> Now, the question is, why parmchk is getting this extra dihedral?
>
> Many thanks for your attention,
>
> Alan
>
> On 26 September 2010 14:56, case <case.biomaps.rutgers.edu> wrote:
>
> > On Sat, Sep 25, 2010, Alan wrote:
> >
> > > First, I am not using ff10 for simulations. My interest is Antechamber
> > (as
> > > it is the core of ACPYPE). I am testing ff10 to validate according my
> > > criteria (still working on a paper to be published) and doing so I hope
> > to
> > > help improve AmberTools.
> >
> > OK...I understand now what you are after. The point is that the "-at
> > amber"
> > flag in Antechamber cannot be used with parm10.dat. Antechamber doesn't
> > know
> > about changing C-alpha atoms in proteins to atom type "CX". The
> parm10.dat
> > parameters should only be used in conjunction with the corresponding
> > "10" library files.
> >
> > In addition, I worry about the "-at amber" flag in general. Antechamber
> > development has been primarily devoted to the GAFF force field. The "-at
> > amber" option is only useful in certain, very restricted cases--basically
> > when the molecule in question is a *small* modification of something
> > appears in
> > proteins or nucleic acids, so that using Amber atom types might be a
> better
> > option than GAFF. Amber atom types are *very* limited -- even seemingly
> > minor changes in the bonding environment might lead to dramatically bad
> > behavior.
> >
> > Second: although this is probably not stated well in the documentation,
> > there
> > will almost certainly need to be hand-editing of results that use this
> > flag.
> > There is no automated way of generating charges that match the Amber ff.
> > R.E.D. might help, but for small changes from existing amino acids or
> > nucleotides, one might really want to (somewhat arbitrarily) restrict the
> > charge changes to a small region of the molecule. This will almost
> > certainly
> > involve hand-work and subjectivity.
> >
> > >
> > > One point of this exercise is to know how good is Antechamber in
> > reproducing
> > > results for which we know the results.
> >
> > This does need to be checked (better than it has been), or else the "-at
> > amber" flag is broken. But in this context, "amber" refers to the atom
> > types
> > in parm94/99. As we add new atoms types (e.g. CI in parmbsc0, or CX in
> > parm10) the antechamber code itself will need to be modified if
> > compatibility
> > is to be maintained.
> >
> > >
> > > Case 1: Using ff99SB/ff99bsc0 (they gave the same result)
> > >
> > >
> > > So I believe antechamber is generating this particular class of
> dihedrals
> > > wrongly.
> >
> > Antechamber doesn't generate dihedrals, good or bad. That is done by
> leap.
> > In you example, you need to compare the atom types in HHH_gas_amber.mol2
> > with
> > the atom types in the standard Amber libraries.
> >
> > >
> > > End of Case 1
> > >
> > >
> #------------------------------------------------------------------------
> > > Now Case 2: Running example above for ALA (AAA) and comparing ff99SB x
> > ff10
> > >
> >
> > > So, AAA ff10_ref works fine because when creating AAA, it gets CX atom
> > type
> > > instead of CT.
> > > However, when using Antechamber, atom type identified is CT
> >
> > The options here are (1) don't use antechamber with ff10; (2) change the
> > antechamber code (e.g. with a "-at amber10" flag), so that it creates the
> > same atom types as are in the library files for ff10.
> >
> > Thanks for the detailed information and tests. Right now, as you have
> > found,
> > the "-at amber" flag is no substitute for having the "real" library
> files.
> > But it could come closer than it does.
> >
> > ....regards...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Sep 29 2010 - 06:00:06 PDT
