VMD-L Mailing List

From: Anurag Sharma (Anurag.Sharma_at_my.ndsu.edu)
Date: Thu Jun 13 2013 - 12:24:09 CDT

Hi Subbarao,

    In my model I have not encountered that problem. Coordinates in merged file are good. My concern now is would it be correct to put value of CA CA CA CA = 0 or not.

Thanks

Anurag

________________________________
From: Subbarao Kanchi [ksubbu85_at_gmail.com]
Sent: Thursday, June 13, 2013 11:24 AM
To: Anurag Sharma
Cc: John Stone; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: error in merging two structures

Hi anurag and john,
                           I face this problem long back. solution is very easy. If you merge file1 (.psf .pdb) and file2 (.psf .pdb) in VMD, you will get merged.psf and merged.pdb. The problem is that CA atom coordinates becomes (0 0 0) that is why structure seems to be corrupted. The solution that I find for this problem is you can mix the two .pdb files by the command "cat" in LINUX terminal.
                           i.e cat file1.pdb file2.pdb > merged.pdb

Then remove the intermediate text lines in between two files in the merged.pdb and later load in VMD along with merged.psf
you can save coordinates merged.pdb again to get the correct (continuous) index numbers for atoms.

Cheers!!!!
SUBBU.