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
www.hpc.co.jp
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Received on Mon Aug 26 2013 - 20:30:03 PDT
