From: Peter Freddolino (
Date: Tue Sep 25 2007 - 21:05:12 CDT

Hi Dhiraj,

Dhiraj Srivastava wrote:
> Is it safe to remove Internal coordinate table of some residue from
> the topology file?
-Removing some parts of the IC table is going to be safe iff you
minimize and only a few atom coordinates are not present, particularly
if only hydrogens are affected. You're going to end up with some guessed
coordinates, but these should relax fairly easily
> also when i am taking out topology information for NAD from the
> topology file /linux/src/vmd-1.8.6
> /plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp and
> puting it in to another file, then this new file is not working and
> when i am using this file in psfgen then psfgen is complaining that
> atom type HN1 not found.
> why is this happening? i was thinking that we can use topology of
> every residue independently.
-All topology files can be used independently so long as MASS lines are
present for all atom types in any of the used topology entries (see the
top of the files). This does *not* apply to stream files, which have
additional prerequisite topology files (read the comments at the top of
the stream files for details)