Writing pdb file.. easier way?

From: Uday Chippada (chippada_at_eden.rutgers.edu)
Date: Thu Nov 18 2004 - 15:58:20 CST

I have another simple question. If I have a pdb file of the sort shown below, and I have to change the residue numbers from say 301 to 401, 302 to 402 and so on, is there a simple way to do it using VMD or any text commands? I have tried cat filename.pdb | awk '{print $1 $2 $3 $4 $5 $6+100 ... }' > newfile.pdb

But this new file is not being read by VMD, must be the format error (the spacings between different columns in the line). Is there a way in which I can get a nice spacing, like how we get when we use the "writepdb" ?

I need to change the residue numbers as I was trying to merge different files with same resid numbers, but different coordinates.

Thanx

Uday

ATOM 1 N PRO A 301 -7.354 25.615 61.612 1.00 26.07

ATOM 2 CA PRO A 301 -6.259 25.170 60.715 1.00 25.38

ATOM 3 C PRO A 301 -6.330 25.908 59.378 1.00 24.47

ATOM 4 O PRO A 301 -7.381 26.437 59.009 1.00 24.48

ATOM 5 CB PRO A 301 -6.398 23.670 60.496 1.00 25.97

ATOM 6 CG PRO A 301 -7.798 23.365 61.012 1.00 26.29

ATOM 7 CD PRO A 301 -8.264 24.501 61.935 1.00 26.63

ATOM 8 N HYP A 302 -5.206 25.961 58.640 1.00 23.36

ATOM 9 CA HYP A 302 -5.175 26.645 57.342 1.00 21.80

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