Hi,
you are right, from reading only the text files there is no apparent way
to be sure. But you could of course load up both your ligand.pdb and
prepin into leap, look at the molecules and identify which atom is which
manually (use xleap instead of tleap and the 'edit' command, or another
viewer like vmd, rasmol, etc.). I realize that this is annoying for one
ligand, tedious for ten and impossible for a thousand, but I'm afraid this
is a limitation of leap at the moment.
Regards,
Thomas
> I understand that I need to change the atom names of MOL in my complex pdb
> so that the atom names are equivalent to that in prp.prepin file. But how
> do
> I s do so?
> The ordering is different with H's inserted between them.
>
> Like...
>
> In prp.prepin file:
>
> 4 *C1* cc M 3 2 1 1.540 111.208 180.000 -0.129681
> 5 H3 ha E 4 3 2 1.070 142.308 -177.898 0.150833
> 6 *C2* cd M 4 3 2 1.331 90.646 0.344 -0.129681
> 7 H4 ha E 6 4 3 1.070 127.188 -178.398 0.150833
> 8 *C3* cd M 6 4 3 1.470 106.080 1.154 -0.119611
> 9 *N1* nc M 8 6 4 1.300 112.000 -0.240 0.027748
> 10 *C5* cc M 9 8 6 1.393 106.304 0.206 -0.119611
> 11 *C4* cf M 10 9 8 1.354 126.020 -179.902 0.164181
> 12 *C21 * ca S 11 10 9 1.507 118.141 -179.870 0.470007
> 13 *C22 * ca B 12 11 10 1.395 120.992 90.681 -0.396821
> 14 C23 ca B 13 12 11 1.372 119.574 179.842 0.105984
> 15 N5 na B 14 13 12 1.339 121.297 -0.195 0.060298
>
> In complex pdb:
>
> HETATM 1 *C * MOL 1 -4.017 -15.843 2.209 1.00 -0.10
> .035 C
> HETATM 2 *C* MOL 1 -4.354 -14.645 2.734 1.00 -0.10
> .035 C
> HETATM 3 *C* MOL 1 -4.335 -13.691 1.625 1.00 0.20
> .070 C
> HETATM 4 *N * MOL 1 -3.975 -14.303 0.458 1.00 -0.60
> .247 N
> HETATM 5 *C* MOL 1 -3.402 -16.640 -0.116 1.00 0.00
> .030 C
> HETATM 6 *C* MOL 1 -3.793 -15.618 0.781 1.00 0.20
> .070 C
> HETATM 7 *C* MOL 1 -3.085 -16.472 -1.477 1.00 0.30
> .046 C
> HETATM 8 *C* MOL 1 -2.761 -17.500 -2.426 1.00 -0.10
> .033 C
> HETATM 9 N MOL 1 -3.060 -15.282 -2.166 1.00 -0.70
> .355
> N
>
> So will I change manually to C1,C2,C3,N1,C5,C4,C21,C22, but the next C is
> missing in prp.prepin file, then how should I number it?
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Apr 21 2010 - 04:30:04 PDT
