You have now a very good suggestion from Thomas regarding how to do it. This
is again what I told you. Simplifying again---
Open two xleap windows. In one, open .prepin file and in another your pdb
file. Compare the atom names in both windows and make the file similar by
manually editing the pdb file.
Hope you have now no doubts!
On Wed, Apr 21, 2010 at 4:35 PM, N.R. Jena <nrjena.gmail.com> wrote:
> 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
>
--
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
