VMD-L Mailing List

From: leila karami (karami.leila1_at_gmail.com)
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