Hi Jason,
I just checked the two parameter files (parm99.dat vs. parm_Frosst.frcmod),
and unless I overlook something major, I am pretty relaxed about the
overwriting of parameters. First, parm_Frosst defines a number of additional
atom types, I cant see any "old" type being hijacked for a "new" one. Second,
most cases where parm99 FF parameters are overwritten, the changes are minor
- often it's a just slight change of the equilibrium bond length / angle.
Other changes relate to parameters which were (if I remember correctly) set
to some reasonable default parameter in parm94 and never changed since then
(and again, in many of the cases the parm99 and pfrosst parameters are
close). Yet another set of changes are parameters Junmei put in which
(probably, I haven't checked every single one) do not occur in natural amino
acids, so this wouldn't affect protein MDs (or hthe protein part in an
prot/lig MD). And for ligands, you have been on your own in the past anyways
(in my experience a much more serious source of errors!)...I have attached a
diff-log for the two FF sets so you can judge yourself.
Bottom line: I think using parm99 together with pfrosst should be fine (and
if I understand the documentation of parm.frosst correctly, this is exactly
what the Merck people did over the last N years), and my feeling is that
there are other errors that are much more serious than those resulting from
overwriting some (ligand) parm99 parameters...although I second Dave's
comment that one should think about a global name space, especially if one
needs to add more parameters/atom types in the future.
And yes, an ANTECHAMBER.ATOMTYPE.DEF file would be great, however, some of
the typing rules are ambiguous, probably as many of the rules and the
parameters have added on the fly during project work where not too much time
could be spend to make sure everything is consistent (I know this way of
working all too well) - there are major issues with bridgeheads in annellated
aromatic rings, or the handling of positive nitrogens - , so the main issue
is in my view to come up with
a consistent set of rules...but this would probably need the help of the
MFrosst people who now work elsewhere...dont know how to proceed from here...
Best,
Th.
pf : C -C 469.0 1.400 RHF/6-41G(d,p) Dec 12 1997
amber: C -C 310.0 1.525 Junmei et al, 1999
pf : C -OS 320.0 1.340 force ff94 CT-OS ; R0 xray
amber: C -OS 450.0 1.323 Junmei et al, 1999
pf : CA-CM 317.0 1.485 CHANGED FROM ff94 ; for the phe-db single bond
amber: CA-CM 427.0 1.433 JCC,7,(1986),230; CYT
pf : CM-OS 300.0 1.400 from CA-OS ** Gro, JACS,V112,4165('90); R0
from a Merck X-ray
amber: CM-OS 480.0 1.240 Junmei et al, 1999
pf : CT-N3 387.6 1.445 calc .B3PW91/6-31G(d) multi system average
amber: CT-N3 367.0 1.471 JCC,7,(1986),230; LYS
pf : CT-OS 320.0 1.370 ** Gro, JACS,V112,4165('90); R0 from a Merck
X-ray
amber: CT-OS 320.0 1.410 JCC,7,(1986),230; NUCLEIC ACIDS
pf : C -C -O 70.0 120.00 RHF/6-41G(d,p) Dec 12 1997
amber: C -C -O 80.0 120.00 Junmei et al, 1999 acrolein
pf : CT-C -CT 70.0 120.00 RHF/6-41G(d,p) Dec 12 1997
amber: CT-C -CT 63.0 117.00 Junmei et al, 1999
pf : CT-C -OS 70.0 120.00
amber: CT-C -OS 80.0 115.00 Junmei et al, 1999
pf : H5-C -N 40.0 120.00 std aromatic
amber: H5-C -N 50.0 120.00 Junmei et al, 1999
pf : H5-C -O 40.0 120.00 std aromatic
amber: H5-C -O 50.0 119.00 Junmei et al, 1999
pf : H5-C -OS 50.0 120.00 std sp2 carbon Dec 18 2000
amber: H5-C -OS 50.0 107.00 Junmei et al, 1999
pf : O -C -OS 70.0 120.00 std aromatic Dec 15 2000
amber: O -C -OS 80.0 125.00 Junmei et al, 1999
pf : CA-CB-CB 63.0 122.700 ff94 CA-CN-CB; AA trp
amber: CA-CB-CB 63.0 117.30 changed from 85.0 bsd on C6H6 nmodes;
NA ade
pf : CA-CB-NB 70.0 132.800 ff94 CA-CN-NA; AA trp
amber: CA-CB-NB 70.0 132.40
pf : CB-CB-NB 70.0 104.400 ff94 CB-CN-NA; AA trp
amber: CB-CB-NB 70.0 110.40
pf : CT-CC-CW 70.0 125.00 ff94 CT-C*-CW; AA trp
amber: CT-CC-CW 70.0 120.00 AA his
pf : CM-CM-OS 70.0 120.00 guess april 11 2000
amber: CM-CM-OS 80.0 125.00 Junmei et al, 1999
pf : H4-CM-OS 50.0 120.00 guess april 11 2000
amber: H4-CM-OS 50.0 113.00 Junmei et al, 1999
pf : HA-CM-HA 40.0 120.00 std aromatic
amber: HA-CM-HA 35.0 120.00 Junmei et al, 1999
pf : C -CT-OS 50.0 109.500 ff94 general CT-X
amber: C -CT-OS 60.0 109.50 Junmei et al, 1999
pf : CM-CT-CT 63.0 114.00 ff94 CA-CT-CT
amber: CM-CT-CT 63.0 111.00 Junmei et al, 1999 (last change:
Mar24,99)
pf : F -CT-F 70.0 109.500 std CT
amber: F -CT-F 77.0 109.10 JCC,13,(1992),963;
pf : OS-CT-OS 70.0 109.500 guess april 11 200
amber: OS-CT-OS 160.0 101.00 Junmei et al, 1999
pf : CT-N3-CT 115.0 110.00
amber: CT-N3-CT 50.0 109.50 AA pro/nt
pf : CW-NA-H 50.0 123.100 indole, ff94 CW-NA-H
amber: CW-NA-H 50.0 120.00 AA his, changed based on NMA nmodes
pf : CA-OH-HO 40.0 113.00 ff94 C-OH-HO
amber: CA-OH-HO 50.0 113.00 replacement in tyr
pf : C -OS-CT 46.5 113.00 ff94 CA-OS-CT
amber: C -OS-CT 60.0 117.00 Junmei et al, 1999
pf : CM-OS-CT 46.5 113.00 from CA-OS-CT ** Gro, JACS,V112,4165('90)
amber: CM-OS-CT 60.0 117.00 Junmei et al, 1999
pf : CT-OS-P 70.0 120.00 RHF/6-31G(d,p) Sept 9 2009
amber: CT-OS-P 100.0 120.50
pf : O2-P -OS 148.0 108.00 RHF/6-31G(d,p) Sept 9 2009
amber: O2-P -OS 100.0 108.23
DIHEDRALS
pf : X -C -C -X 4 2.50 180.000 2 gentle planar from
X-CP-CP-X
amber: X -C -C -X 4 14.50 180.0 2. Junmei et al,
1999
Mit freundlichen Grüßen / Kind regards,
Dr. Thomas Fox
Boehringer Ingelheim Pharma GmbH & Co. KG
Dept. Lead Identific. and Optim. Sup. Ge
Tel.: +49 (7351) 54-7585
Fax: +49 (7351) 83-7585
mailto:thomas.fox.boehringer-ingelheim.com
Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim
Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender),
Ursula Fuggis-Hahn, Ralf Gorniak, Michael Klein, Dr. Martin Wanning;
Vorsitzender des Aufsichtsrates: Prof. Dr. Dr. Andreas Barner; Sitz:
Ingelheim am Rhein; Registergericht Mainz: HR B 23260
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-----Ursprüngliche Nachricht-----
Von: Jason Swails [mailto:jason.swails.gmail.com]
Gesendet: Dienstag, 7. Februar 2012 19:33
An: AMBER Mailing List
Betreff: Re: [AMBER] parm.frosst parameters
On Tue, Feb 7, 2012 at 1:16 PM, Guanglei Cui
<amber.mail.archive.gmail.com>wrote:
> Tom and Dave,
>
> I found Parm.Frosst was released to CCL.net (Google knows it all). If
> you follow the link below, you can download the parm/frcmod files and
> some test sets. The atom types are the upper case Amber types (not
> gaff).
Then how do we avoid parm.frosst parameters from overwriting the Amber
protein parameters? I've looked at the parm files and they declare some of
the same atom types that Amber uses for their force fields...
Or is this not supposed to be used with Amber force fields in the same
topology?
> One way to use it in MD is to use MOE to assign atom types and
> save it to a mol2 file. Unfortunately, MOE doesn't save the assigned
> atom types. One has to modify it manually to the corresponding
> Parm.Frosst types.
>
> I haven't used it for real. I'm not aware if anyone else at GSK is
> testing it. It'll be great if we can share our experience here.
>
> http://www.ccl.net/cca/data/parm_at_Frosst/
>
> Regards,
> Guanglei
>
> On Sun, Feb 5, 2012 at 9:11 AM, case <case.biomaps.rutgers.edu> wrote:
> > On Wed, Feb 01, 2012, thomas.fox.boehringer-ingelheim.com wrote:
> >>
> >> is anybody working on implementing Chris Bayly's parmfrosst force field
> in
> >> antechamber? It seems there are a number of issues and inconsistencies
> that
> >> probably should be resolved to avoid a number of "almost parm.frosst"
> force
> >> fields where everybody has changed/improved things differently. Please
> >> contact me offline for more details.
> >> Chris - I don't have your current e-mail address, if you read this:
> can you
> >> drop me a line?
> >>
> >
> > I'm guessing that in fact no one is working on this right now. You might
> > try to contact Junmei Wang directly (junmwang.yahoo.com), since he often
> > doesn't follow this reflector.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> Guanglei Cui
>
> _______________________________________________
> 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
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Received on Tue Feb 14 2012 - 08:00:03 PST
