VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Wed Aug 22 2007 - 09:30:57 CDT

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 

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