VMD-L Mailing List

From: Sergio Anis (sergioanis_at_ispwest.com)
Date: Mon Sep 12 2005 - 22:07:04 CDT

 
 hi everybody;

I'm having problems writing a pdb file. First, let me tell you what I'm
doing:

1) load 2 molecules (mol1: 'protein + heteroatom1'; mol2: 'heteroatom2')
2) align 'heteroatom1' and 'heteroatom2'
3) write a pdb file with the coordinates of 'protein + heteroatom2'

That is: replacing heteroatom1 by heteroatom2

Here is what I tried:

1) write a pdb with the coordinates of 'protein' and another pdb with the
coordinates of 'heteroatom2'
2) use the script 'mergepdbs.tcl'
I get this error message:

building segment V1
setting patch for first residue to NONE
setting patch for last residue to NONE
reading residues from pdb file mimic2.pdb
unknown residue type HEM
extracted 1 residues from pdb file
Info: generating structure...
unknown residue type HEM
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

Another approach:
1) manually paste heteroatom2 at the end of protein (making the appropriates
changes like TER by END -at the end of the protein- and keep adding the
number of the atom -the number right after the word HETATM-; at one point I
even added the CONECT info for the heteroatom)
When I load this pdb file I don't get the heteroatom. I get the following
messages (several time each):

error> residue exceeded maximum number of bonds (4)
warning> unusual bond between residues .... and ....

But if I open protein or heteroatom2 alone I don't have any problem

I appreciate any advice you can give me

thanks,

Sergio