Re: How to patch residues in different chains

From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon Apr 10 2006 - 11:25:59 CDT

I did same but it is giving error when I am using a patch. Following
is my PDB complex. I am trying to generate a psf file for this
complex.
-------------------------------
ATOM 3583 N THR C 156 41.313 35.020 61.047 1.00 93.28 N
ATOM 3584 CA THR C 156 41.803 34.746 59.708 1.00 93.42 C
ATOM 3585 C THR C 156 41.070 35.567 58.658 1.00 93.24 C
ATOM 3586 O THR C 156 39.843 35.532 58.565 1.00 93.27 O
ATOM 3587 CB THR C 156 41.674 33.242 59.383 1.00 94.14 C
ATOM 3588 OG1 THR C 156 42.410 32.482 60.354 1.00 94.44 O
ATOM 3589 CG2 THR C 156 42.224 32.938 58.000 1.00 94.17 C
TER
ATOM 2103 N GLY D 156 69.980 32.099 23.275 1.00 74.53 N
ATOM 2104 CA GLY D 156 69.452 33.322 22.695 1.00 80.51 C
ATOM 2105 C GLY D 156 70.075 34.593 23.225 1.00 84.25 C
ATOM 2106 O GLY D 156 70.716 35.323 22.474 1.00 85.87 O
ATOM 2107 N GLY D 167 69.879 34.867 24.509 1.00 88.22 N
ATOM 2108 CA GLY D 167 70.432 36.076 25.093 1.00 94.22 C
ATOM 2109 C GLY D 167 69.678 37.341 24.719 1.00 98.80 C
ATOM 2110 O GLY D 167 70.163 38.451 24.951 1.00 98.67 O

> > patch DISU 1a2d 119 1a2d:200 etc
> >
> > but in my protein both chains are different( like A and B ). Any help
>
> You should read each chain as a different segment. If you read chain A
> as segment AA and chain B as segment BB, and want to link residue 10 in
> chain A to residue 20 in chain B, you'll have something like:
>
> patch DISU AA:10 BB:20
>
> Leo
>
> --
> Leonardo Giantini Trabuco
> Ph.D. student
> Center for Biophysics and Computational Biology
> University of Illinois at Urbana-Champaign
>

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