VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon May 05 2008 - 00:18:00 CDT

The O is actually the chain name, not part of the resname. Since pdbs have
a fixed-width format, there is sometimes no spaces between columns.

 

See here for more details:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node2
0.html

 

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
cong chen
Sent: Monday, May 05, 2008 12:09 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: about writepdb

 

Dear all,

    I want to save the coordinates of current frame into a pdb file and I
did it successfully using the command "Save Coordinates..." under the menu
"File".

However, I found that the molecule type name has been changed. The following
is a single line of the pdb file:

ATOM 1 OH2 SPCEO 1 20.111 5.826 32.502 1.00 0.00 O1

The molecule type name part is "SPCEO" . But in the psf file, the type name
of the same molecule is "SPCE". I wonder why the vmd adds a character "O" ?
For molecule number larger than 1000, the molecule type name part and the
molecule number part will join together like this:

ATOM 5341 OH2 SPCEO1781 19.493 2.835 31.522 1.00 0.00 O1

I want to know how to tell VMD NOT to change the molecule type name.

Any suggestions would be most appreciative.

Thank you.

 

  

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