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: [EMAIL PROTECTED] skype: vvchaban _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
