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
>
>
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> 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<<
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Received on Wed Sep 29 2010 - 05:00:08 PDT
