From: leila karami (
Date: Sat Dec 25 2010 - 09:14:57 CST

Dear VMD users

happy christmas

I did simulation of protein-dna complex in water solvent (TIP3P). I
converted gromacs trajectory file (xtc) to amber trajectory
file (mdcrd) by VMD. when I see converted mdcrd file by vmd, protein and dna
are normal but there is a problem about
water molecules: 1) the length of O-H bonds are longer than those of normal
waters. 2) there are new bonds between H atoms
of each water molecule.

is this state normal? is it a visual program? Do trajectory file conversion
done correctly?

how to fix it?

any help will highly appreciated

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group