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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Feb 14, 2012, at 10:49 AM, <thomas.fox.boehringer-ingelheim.com> wrote:
> 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;
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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
>>>
>>>
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> Guanglei Cui
>>
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>>
>
>
>
> --
> 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
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Received on Tue Feb 14 2012 - 15:30:02 PST