Dear Jacob,
> I have downloaded a DNA pdb and then loaded it in xleap:
>
> xleap
>> source leaprc.gaff
>> source leaprc.ff99bsc0
>> v = loadpdb dna.pdb
>> savemol2 v dnamol.mol2 0
>> quit
> I am getting file as in the format:
> .<TRIPOS>MOLECULE
> default_name
> 758 816 24 0 1
> SMALL
> USER_CHARGES
> .<TRIPOS>ATOM
> 1 HO5' 18.422427 34.965199 25.873245 HO 1 DC5 0.4422 ****
[...]
> 758 HO3' 19.009850 19.050156 31.922063 HO 24 DG3 0.4396 ****
> .<TRIPOS>BOND
> 1 28 29 1
[...]
> 816 725 728 1
> .<TRIPOS>SUBSTRUCTURE
> 1 DC5 1 **** 0 **** ****
> 2 DG 29 **** 0 **** ****
> 3 DC 62 **** 0 **** ****
> 4 DG 92 **** 0 **** ****
> 5 DA 125 **** 0 **** ****
> 6 DA 157 **** 0 **** ****
> 7 DT 189 **** 0 **** ****
> 8 DT 221 **** 0 **** ****
> 9 DC 253 **** 0 **** ****
> 10 DG 283 **** 0 **** ****
> 11 DC 316 **** 0 **** ****
> 12 DG3 346 **** 0 **** ****
> 13 DC5 380 **** 0 **** ****
> 14 DG 408 **** 0 **** ****
> 15 DC 441 **** 0 **** ****
> 16 DG 471 **** 0 **** ****
> 17 DA 504 **** 0 **** ****
> 18 DA 536 **** 0 **** ****
> 19 DT 568 **** 0 **** ****
> 20 DT 600 **** 0 **** ****
> 21 DC 632 **** 0 **** ****
> 22 DG 662 **** 0 **** ****
> 23 DC 695 **** 0 **** ****
> 24 DG3 725 **** 0 **** ****
>
> Here this **** symbol is ok?
Yes
> I mean in general, this stars are not there in
> the mol2 file but is it ok in my case?
Yes - each program adapts the mol2 file format; same 'problem' with
the PDB file format...
> I tried to perform MD simulation
> with this mol2 file and there was no problem in the MD simulation.
No it looks like all is ok ;-)
> Moreover, is partial charges are listed in the last column?
Yes
See also:
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
regards, Francois
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Received on Fri Mar 20 2015 - 03:30:04 PDT
