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
>
--
ＨＰＣシステムズ株式会社 （ http://www.hpc.co.jp/ ）
HPC事業部 技術グループ 渡邊 啓正 <hi-watanabe.hpc.co.jp>
〒108-0022 東京都港区海岸3-9-15 LOOP-X 8階
TEL：03-5446-5530（代表）／FAX：03-5446-5550（共通）
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
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Received on Sun Aug 18 2013 - 18:00:02 PDT
