Hello Anton,
maybe I don't fully understand your problem. But with VMD you can
select and display any desired molecule/atom subset of a larger system using the graphics
menu. You can even create several subsets of molecules and/or
atoms and use a different gaphical representation or coloring method for
each. The manual at the VMD homepage describes how to create subsets
in detail: http://www.ks.uiuc.edu/Research/vmd/current/ug/node40.html
Hope that helps
Florian
ABG> Dear Amber Users,
ABG> I would like to create a movie based on MD trajectory for only a
ABG> subset of atoms. Let say RES 1-5 and a couple of solvent molecules
ABG> out of system with 240 residues in a water box. The programs i used
ABG> so far let me do it only if I recreate the new topology (or .parm in case
ABG> of VMD) file and load it together with the new (modified) coordinate
ABG> stream.
ABG> Is there any way to do it without creating a new .top file?
ABG> Thanks a lot,
ABG> Anton
ABG> *******************************
ABG> * Anton B. Guliaev, Ph.D *
ABG> * Life Sciences Division *
ABG> _ * LBNL, Berkeley CA 94720 * _
ABG> / )* abguliaev_at_lbl.gov *( \
ABG> / / * F:(510)-486-6488 * \ \
ABG> _( (_ * T: 510-486-5773 * ) )_
ABG> (((\ \)**/ )*********************( \**(/ /)))
ABG> (\\\\ \_/ / \ \_/ ////)
ABG> \ / \ /
ABG> \ _/ \_ /
ABG> / / \ \
ABG> /___/ \___\
____________________________________
Florian Barth
Institute of Technical Biochemistry
University of Stuttgart
Allmandring 31
70569 Stuttgart
Germany
phone: +49-711-6857481
fax: +49-711-6853196
E-mail: bio_hazard_at_gmx.de
WWW: http://www.itb.uni-stuttgart.de
Received on Thu Aug 30 2001 - 14:16:00 PDT
