Dear Dr. Case,
My apologies for my non-effective example.
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
:
(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
:
----
Best regards,
WATANABE
> On Mon, Aug 12, 2013, Hiromasa WATANABE wrote:
>>
>> antechamber sometimes generates different(wrong) atom types and
>> force field parameters even if we use same molecule structures.
>> Results with AmberTools12 are as follows:
>>
>> (molecule 1)
>> cc
>> cd h4
>> cc c2
>> cd oh ho
>> cc
>>
>>
>> (molecule 2, which is created by shuffling lines of molecule 1)
>> cd
>> cc h4
>> cd c2
>> cc oh ho
>> cd
>>
>> Would you let me know why this happens?
>> What should I do for getting right result?
>
> I don't see anything wrong here, at least that is very obvious. Can you be
> more explicit about what problem you see? (Swapping "cc" and "cd" should have
> no effect.)
>
> ...dac
>
>
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--
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 12 2013 - 23:00:01 PDT
