From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 22 2007 - 13:54:14 CDT

Tom,
  The order in which files are added to a molecule in VMD has a strong
effect on the contents of the molecule when you're done. In the current
versions of VMD, information like the atom name, atom type, residue name,
residue ID, chain, and segment name are determined entirely by the first file
loaded. We may change VMD to allow overriding of these fields by
subsequently loaded files, when requested by the user, but at the moment,
the "first file loaded wins" for those fields IIRC. Other structure data
like element type, bonds, charges, masses, etc may be replaced by
subsequently loaded files depending on the plugin/format being read in.

The current implementation isn't as flexible as we'd like, so there are
cases that can be problematic, but I'm working on it...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 22, 2007 at 09:30:57AM -0500, Thomas C. Bishop wrote:
> Dear VMD,
>
> As you well know amber does not store chain/segname information in it's
> parm/top/crd files.
>
> So if I ask you to display a molecule as
>
> vmd -parm7 mol.parm7 -crd mol.crd
> or
> vmd -parm7 mol.parm7 -pdb mol.pdb
> then you have no idea about chain or segnames
>
> However if I swap the order of loading as follows...
>
> vmd -pdb mol.pdb -parm7 mol.parm7
>
> AND mol.pdb contains segname and chain information. It appears that you
> do read segname,chain name and give your best guess for a molecular
> topology before reading the topology and other information from the
> parm7
>
>
> So now my question... what is the complete list of information (bonds,
> angles, altloc, etc..) effected when I load parm7/pdb files in reverse
> order ?
>
> For now it seems like a slick trick to get around the problem with amber
> parm files not including segnames, chains and other info.
> BUT what bugs are waiting to bite me?
>
> Granted my mol.pdb has to be consistent w/ mol.parm7
> (For this reason I have tleap make a pdb when it makes the parm7/crd
> pair and then simply reload my chain/segnames into this pdb)
>
>
> Thanks
> TOm
>
>
>
> --
> ***********************
> * Thomas C. Bishop *
> *Office: 504-862-3370 *
> *CCS: 504-862-8391 *
> *Fax: 504-862-8392 *
> ***********************

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078