[gmx-users] Re: force field for boron-nitride nanotube
Vitaly Chaban
chaban at univer.kharkov.ua
Mon Sep 8 12:37:13 CEST 2008
Of course, there exist a bunch of works simulating B-N NTs. See
papers.
PDB file isn't enough to make a topology for gromacs.
gurgo> Has anything like that ever been simulated? If it hasn't, there may not be
gurgo> paramteers for such a species. I don't believe boron exists as an atom type in
gurgo> any of the force fields provided by Gromacs.
gurgo> If all of the above is true, you will have the (very hard) task of deriving new
gurgo> parameters for your nanotube.
gurgo> -Justin
>> The pdb file of nanotube is as follow:
>> HETATM 1 N1 UNK 1 1.597 0.000 -5.015 1.00
>> 0.00 N
>> HETATM 2 N2 UNK 1 1.129 1.129 -2.870 1.00
>> 0.00 N
>> HETATM 3 B3 UNK 1 1.129 1.129 -4.291 1.00
>> 0.00 B
>> HETATM 4 N4 UNK 1 0.000 1.597 -5.015 1.00
>> 0.00 N
>> HETATM 5 N5 UNK 1 -1.129 1.129 -2.870 1.00
>> 0.00 N
>> HETATM 6 B6 UNK 1 -1.129 1.129 -4.291 1.00
>> 0.00 B
>> HETATM 7 N7 UNK 1 -1.597 0.000 -5.015 1.00
>> 0.00 N
>> HETATM 8 N8 UNK 1 -1.129 -1.129 -2.870 1.00
>> 0.00 N
>> HETATM 9 B9 UNK 1 -1.129 -1.129 -4.291 1.00
>> 0.00 B
>> HETATM 10 N10 UNK 1 0.000 -1.597 -5.015 1.00
>> 0.00 N
>> HETATM 11 N11 UNK 1 1.129 -1.129 -2.870 1.00
>> 0.00 N
>> HETATM 12 B12 UNK 1 1.129 -1.129 -4.291 1.00
>> 0.00 B
>> HETATM 13 N13 UNK 1 1.597 0.000 -0.724 1.00
>> 0.00 N
>> HETATM 14 B14 UNK 1 1.597 0.000 -2.145 1.00
>> 0.00 B
>> HETATM 15 N15 UNK 1 1.129 1.129 1.421 1.00
>> 0.00 N
>> HETATM 16 B16 UNK 1 1.129 1.129 0.000 1.00
>> 0.00 B
>> HETATM 17 N17 UNK 1 0.000 1.597 -0.724 1.00
>> 0.00 N
>> HETATM 18 B18 UNK 1 0.000 1.597 -2.145 1.00
>> 0.00 B
>> HETATM 19 N19 UNK 1 -1.129 1.129 1.421 1.00
>> 0.00 N
>> HETATM 20 B20 UNK 1 -1.129 1.129 0.000 1.00
>> 0.00 B
>> HETATM 21 N21 UNK 1 -1.597 0.000 -0.724 1.00
>> 0.00 N
>> HETATM 22 B22 UNK 1 -1.597 0.000 -2.145 1.00
>> 0.00 B
>> HETATM 23 N23 UNK 1 -1.129 -1.129 1.421 1.00
>> 0.00 N
>> HETATM 24 B24 UNK 1 -1.129 -1.129 0.000 1.00
>> 0.00 B
>> HETATM 25 N25 UNK 1 0.000 -1.597 -0.724 1.00
>> 0.00 N
>> HETATM 26 B26 UNK 1 0.000 -1.597 -2.145 1.00
>> 0.00 B
>> HETATM 27 N27 UNK 1 1.129 -1.129 1.421 1.00
>> 0.00 N
>> HETATM 28 B28 UNK 1 1.129 -1.129 0.000 1.00
>> 0.00 B
>> HETATM 29 N29 UNK 1 1.597 0.000 3.566 1.00
>> 0.00 N
>> HETATM 30 B30 UNK 1 1.597 0.000 2.145 1.00
>> 0.00 B
>> HETATM 31 B31 UNK 1 1.129 1.129 4.291 1.00
>> 0.00 B
>> HETATM 32 N32 UNK 1 0.000 1.597 3.566 1.00
>> 0.00 N
>> HETATM 33 B33 UNK 1 0.000 1.597 2.145 1.00
>> 0.00 B
>> HETATM 34 B34 UNK 1 -1.129 1.129 4.291 1.00
>> 0.00 B
>> HETATM 35 N35 UNK 1 -1.597 0.000 3.566 1.00
>> 0.00 N
>> HETATM 36 B36 UNK 1 -1.597 0.000 2.145 1.00
>> 0.00 B
>> HETATM 37 B37 UNK 1 -1.129 -1.129 4.291 1.00
>> 0.00 B
>> HETATM 38 N38 UNK 1 0.000 -1.597 3.566 1.00
>> 0.00 N
>> HETATM 39 B39 UNK 1 0.000 -1.597 2.145 1.00
>> 0.00 B
>> HETATM 40 B40 UNK 1 1.129 -1.129 4.291 1.00
>> 0.00 B
>> HETATM 41 H41 UNK 1 -2.140 0.000 -5.855 1.00
>> 0.00 H
>> HETATM 42 H42 UNK 1 0.000 2.140 -5.855 1.00
>> 0.00 H
>> HETATM 43 H43 UNK 1 2.140 0.000 -5.855 1.00
>> 0.00 H
>> HETATM 44 H44 UNK 1 0.000 -2.140 -5.855 1.00
>> 0.00 H
>> HETATM 45 H45 UNK 1 1.582 1.582 5.282 1.00
>> 0.00 H
>> HETATM 46 H46 UNK 1 1.582 -1.582 5.282 1.00
>> 0.00 H
>> HETATM 47 H47 UNK 1 -1.582 1.582 5.282 1.00
>> 0.00 H
>> HETATM 48 H48 UNK 1 -1.582 -1.582 5.282 1.00
>> 0.00 H
>>
>> regards
>>
>> Javad
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
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