Dear Mr. Junmei,
Cc: Dr. Case,
Thank you very much for your reply in detail !
I understood your explanation.
I'm looking forward to the fix.
Best regards,
WATANABE
> Hello, sorry for the late reply, just came back from a trip without internet access.
>
> First of all, the cc/cd, ce/cf atom types are equivalent and therefore the force field parameters involved
> by those atom types should be the same. Also the force field parameters are the same for one molecule no
> matter what atom sequence order it is. However, the atom type assignment with 'atomtype' does depend on
> atom sequence order. Both assignments are correct for your molecule. We introduced the equivalent atom types
> to discriminate conjugated bond from single and double bonds without explicitly using bond type information
> in residue topologies (prepi or prepc files).
>
> To generate force field parameters for bond lengths and bond angles, we did statistics on ab initio
> optimized geometries. Since the assignment to cc/cd, ce/cf, etc, depend on the atom sequence orders, the
> equivalent force field parameters may take different values (the data sets for doing statistics are
> different). We wrote a program to force the equivalent force field parameters to take the same values. For
> some reason (bugs in the program), some equivalent force field parameters still take different values. We
> will fix this problem as soon as possible.
>
> Best
>
> Junmei
>
>
>
> ------------------------------------------------------------------------------------------------------------
> *From:* Hiromasa WATANABE <hi-watanabe.hpc.co.jp>
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Cc:* David A Case <case.biomaps.rutgers.edu>; junmwang.yahoo.com
> *Sent:* Monday, August 26, 2013 10:14 PM
> *Subject:* Re: [AMBER] antechamber returns different results from same molecule structures
>
> Dear Dr. Case and Mr. Junmei,
>
> Please let me know any follow-ups.
> I look forward to your reply.
>
> Best regards,
> WATANABE
>
> > Dear Dr. Case,
> >
> > Thanks for your rapid reply.
> >
> > prep/frcmod files were created by:
> > % antechamber -i input.pdb -fi pdb -o mol.prep -fo prepi -c bcc -nc 0
> > % parmchk -i mol.prep -f prepi -o mol.frcmod
> >
> > > ca-cf-cc 62.810 130.800
> > These values are defined in gaff.dat.
> > Others are given by the frcmod file.
> >
> > Best regards,
> > WATANABE
> >
> >> On Tue, Aug 13, 2013, Hiromasa WATANABE wrote:
> >>>
> >>> Please see another example below.
> >>> I see atom type "ce" in the molecule (1),
> >>> and "cf" in the molecule (2).
> >>> According to that, their force field parameters differ,
> >>> and their equilibrium structure and fluctuation also change.
> >>>
> >>> Do you have any guidelines for getting appropriate force field parameters?
> >>>
> >>> (1)
> >>> HETATM 1 C 0 -0.971 -0.433 -0.171
> >>> HETATM 2 C 0 -1.292 0.879 -0.521
> >>> HETATM 3 C 0 -2.586 1.352 -0.374
> >>> HETATM 4 C 0 -3.580 0.526 0.124
> >>> HETATM 5 C 0 -3.278 -0.786 0.463
> >>> HETATM 6 C 0 -1.989 -1.262 0.309
> >>> HETATM 7 H 0 -0.530 1.526 -0.932
> >>> HETATM 8 H 0 -2.819 2.372 -0.654
> >>> HETATM 9 H 0 -4.590 0.898 0.240
> >>> HETATM 10 H 0 -4.052 -1.439 0.845
> >>> HETATM 11 H 0 -1.759 -2.288 0.569
> >>> HETATM 12 C 0 0.407 -0.993 -0.323
> >>> HETATM 13 H 0 0.436 -2.038 -0.620
> >>> HETATM 14 C 0 1.568 -0.381 -0.110
> >>> HETATM 15 C 0 2.912 -1.003 -0.301
> >>> HETATM 16 C 0 3.844 -0.119 0.021
> >>> HETATM 17 C 0 3.182 1.141 0.460
> >>> HETATM 18 C 0 1.867 0.996 0.384
> >>> HETATM 19 H 0 3.052 -2.013 -0.658
> >>> HETATM 20 H 0 4.916 -0.254 -0.013
> >>> HETATM 21 H 0 3.722 2.016 0.794
> >>> HETATM 22 H 0 1.117 1.720 0.659
> >>>
> >>> (result)
> >>> cd = cc
> >>> / |
> >>> ce = cd |
> >>> / \ |
> >>> ca cd = cc
> >>>
> >>> ca-ce-cd 63.840 119.620
> >>> ca-ce-cd-cd 1 1.000 180.000 2.000
> >>
> >> Where did these values come from? (Parmchk?)
> >>
> >>>
> >>> (2)
> >>> HETATM 14 C 0 1.568 -0.381 -0.110
> >>> HETATM 15 C 0 2.912 -1.003 -0.301
> >>> HETATM 16 C 0 3.844 -0.119 0.021
> >>> HETATM 17 C 0 3.182 1.141 0.460
> >>> HETATM 18 C 0 1.867 0.996 0.384
> >>> HETATM 19 H 0 3.052 -2.013 -0.658
> >>> HETATM 20 H 0 4.916 -0.254 -0.013
> >>> HETATM 21 H 0 3.722 2.016 0.794
> >>> HETATM 22 H 0 1.117 1.720 0.659
> >>> HETATM 12 C 0 0.407 -0.993 -0.323
> >>> HETATM 13 H 0 0.436 -2.038 -0.620
> >>> HETATM 1 C 0 -0.971 -0.433 -0.171
> >>> HETATM 2 C 0 -1.292 0.879 -0.521
> >>> HETATM 3 C 0 -2.586 1.352 -0.374
> >>> HETATM 4 C 0 -3.580 0.526 0.124
> >>> HETATM 5 C 0 -3.278 -0.786 0.463
> >>> HETATM 6 C 0 -1.989 -1.262 0.309
> >>> HETATM 7 H 0 -0.530 1.526 -0.932
> >>> HETATM 8 H 0 -2.819 2.372 -0.654
> >>> HETATM 9 H 0 -4.590 0.898 0.240
> >>> HETATM 10 H 0 -4.052 -1.439 0.845
> >>> HETATM 11 H 0 -1.759 -2.288 0.569
> >>>
> >>> (result)
> >>> cc = cd
> >>> / |
> >>> cf = cc |
> >>> / \ |
> >>> ca cc = cd
> >>>
> >>> ca-cf-cc 62.810 130.800
> >>> cc-cc-cf-ca 1 6.650 180.000 2.000
> >>> :
> >>
> >> Looks like a bug in gaff.dat or parmchk to me (at least my initial
> >> reaction). A cf-cc bond (as I understand it) should be the same as cd-ce,
> >> but it looks like parmchk is not respecting this. (I mention parmchk
> >> since some of the values you cite above don't appear in gaff.dat.)
> >>
> >> Cc-ing to Junmei for comment. These are very tough systems to parameterize
> >> with just bond type assignments, and it looks to me like gaff.dat is
> >> incomplete: some interactions of cc with other atom types are not matched with
> >> equivalent interactions of cd (etc.)
> >>
> >> ...thanks for the report...dac
> >>
> >
>
> --
> Hiromasa WATANABE
> Manager, Ph.D.
> HPC Dept., Technology Gr., HPC SYSTEMS Inc.
> Head office: LOOP-X 8F, 3-9-15 Wangan, Minato-ku, Tokyo, Japan 108-0022.
> Email: hi-watanabe.hpc.co.jp <mailto:hi-watanabe.hpc.co.jp>
> www.hpc.co.jp
>
>
>
>
> __________ Information from ESET NOD32 Antivirus, version of virus signature database 8732 (20130827) __________
>
> The message was checked by ESET NOD32 Antivirus.
>
> http://www.eset.com
--
Hiromasa WATANABE
Manager, Ph.D.
HPC Dept., Technology Gr., HPC SYSTEMS Inc.
Head office: LOOP-X 8F, 3-9-15 Wangan, Minato-ku, Tokyo, Japan 108-0022.
Email: hi-watanabe.hpc.co.jp
www.hpc.co.jp
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 27 2013 - 18:00:04 PDT
