David,
yes both pdb and mol2 (from which lib file have been created) consist of
the same MOL unit
.<TRIPOS>MOLECULE
MOL
21 21 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 C1 -0.8530 0.6970 -0.0090 ca 2767 MOL -0.130000
2 C2 0.5420 0.6970 -0.0090 ca 2767 MOL -0.124000
3 C3 1.2400 1.9050 -0.0090 ca 2767 MOL -0.130000
4 C4 0.5420 3.1130 -0.0100 ca 2767 MOL -0.113000
5 C5 -0.8530 3.1130 -0.0110 ca 2767 MOL -0.099300
6 C6 -1.5510 1.9050 -0.0100 ca 2767 MOL -0.113000
7 H7 -1.4030 -0.2550 -0.0090 ha 2767 MOL 0.133500
8 H8 1.0910 -0.2550 -0.0080 ha 2767 MOL 0.133000
9 H9 2.3390 1.9050 -0.0090 ha 2767 MOL 0.133500
10 H10 1.0920 4.0660 -0.0100 ha 2767 MOL 0.143000
11 H11 -2.6500 1.9050 -0.0100 ha 2767 MOL 0.143000
12 C12 -1.6230 4.4470 -0.0120 c3 2767 MOL 0.181700
13 H13 -1.8180 4.7470 0.9960 h1 2767 MOL 0.044200
14 H14 -1.0370 5.1970 -0.5010 h1 2767 MOL 0.044200
15 O15 -2.8620 4.2810 -0.7080 os 2767 MOL -0.419900
16 C16 -3.5490 5.5340 -0.7640 c 2767 MOL 0.628100
17 O17 -4.6660 5.6190 -1.3360 o 2767 MOL -0.488000
18 C18 -2.9190 6.7840 -0.1230 c3 2767 MOL -0.191100
19 H19 -2.7520 6.6060 0.9190 hc 2767 MOL 0.074700
20 H20 -1.9860 6.9990 -0.6020 hc 2767 MOL 0.074700
21 H21 -3.5800 7.6170 -0.2410 hc 2767 MOL 0.074700
and the ligand.pdb file
ATOM 1 C1 MOL 1 -0.853 0.697 -0.009 1.00 0.00
ATOM 2 C2 MOL 1 0.542 0.697 -0.009 1.00 0.00
ATOM 3 C3 MOL 1 1.240 1.905 -0.009 1.00 0.00
ATOM 4 C4 MOL 1 0.542 3.113 -0.010 1.00 0.00
ATOM 5 C5 MOL 1 -0.853 3.113 -0.011 1.00 0.00
ATOM 6 C6 MOL 1 -1.551 1.905 -0.010 1.00 0.00
ATOM 7 H7 MOL 1 -1.403 -0.255 -0.009 1.00 0.00
ATOM 8 H8 MOL 1 1.091 -0.255 -0.008 1.00 0.00
ATOM 9 H9 MOL 1 2.339 1.905 -0.009 1.00 0.00
ATOM 10 H10 MOL 1 1.092 4.066 -0.010 1.00 0.00
ATOM 11 H11 MOL 1 -2.650 1.905 -0.010 1.00 0.00
ATOM 12 C12 MOL 1 -1.623 4.447 -0.012 1.00 0.00
ATOM 13 H13 MOL 1 -1.818 4.747 0.996 1.00 0.00
ATOM 14 H14 MOL 1 -1.037 5.197 -0.501 1.00 0.00
ATOM 15 O15 MOL 1 -2.862 4.281 -0.708 1.00 0.00
ATOM 16 C16 MOL 1 -3.549 5.534 -0.764 1.00 0.00
ATOM 17 O17 MOL 1 -4.666 5.619 -1.336 1.00 0.00
ATOM 18 C18 MOL 1 -2.919 6.784 -0.123 1.00 0.00
ATOM 19 H19 MOL 1 -2.752 6.606 0.919 1.00 0.00
ATOM 20 H20 MOL 1 -1.986 6.999 -0.602 1.00 0.00
ATOM 21 H21 MOL 1 -3.580 7.617 -0.241 1.00 0.00
as you can see the difference is only to presence of the hydrogens in the
mol2 file which hs been stripped from pdb after docking. Will it be better
to proceed ligand to antechamber AFTER docking (adding hydrogen’s back
using babel for instance) ?
Kind regards,
James
2014-09-17 21:41 GMT+02:00 David A Case <case.biomaps.rutgers.edu>:
> On Wed, Sep 17, 2014, James Starlight wrote:
>
> > Yes sure I've tried to applied parametrization of the ligand.pdb file
> > (stripped from hydrogens) produced by autodock with the tleap and its
> > produced errors that each atom type of the ligand has not been found:
> >
> > Unknown residue: MOL number: 0 type: Terminal/last
>
> This doesn't seem to have anything to do with hydrogens being present or
> not. You appear to have a residue named "MOL" in your input mol2 file,
> but no such residue in any library files you have loaded.
>
> > loadoff /ligand/ligand.lib
>
> Does ligand.lib define the MOL unit? Both atom and residue names have to
> match between libraries and input files.
>
> ...dac
>
>
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Received on Thu Sep 18 2014 - 01:00:02 PDT
