VMD-L Mailing List

From: Maxim Paliy. (mpaliy_at_wlu.ca)
Date: Thu May 14 2009 - 20:01:40 CDT

Dear VMD experts
I want to add a few bonds to my system (join two nucleic backbones)
and then write the corresponding psf via e.g.
set all [atomselect top all]
$all writepsf my.psf

The change in bonding is reflected this way, but the angles and
dihedrals stay intact..

How would I force the angles and dihedrals to update as well?

For some reason, the simplest way
readpsf 1.psf
coordpdb 1.pdb
readpsf 2.psf
coordpdb 2.pdb
writepsf my.psf
writepdb my.pdb
does not work for me (probably because the ends of the chains I want to
join are not well aligned).

 maybe there are some other ways to accomplish this task without writing
all psf file manually?

Thanks a lot in advance for the suggestions,
Maxim