Edit pdb file manually (use xleap to identify atoms) as I told you earlier.
On Wed, Apr 21, 2010 at 4:21 PM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Sir,
>
> 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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--
Nihar Ranjan Jena
Research Scientist,
SERC Fast Track Scheme for Young Scientists (DST)
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore - 560012, India
Web page: http://sites.google.com/site/nrjena/Home
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Received on Wed Apr 21 2010 - 04:30:05 PDT
