[gmx-users] reading Hydrogens from an itp file

gromacs query gromacsquery at gmail.com
Tue Apr 9 11:19:46 CEST 2013


Dear All,

I have a pdb file in which has only heavy atoms (means all atoms except
hydrogen) and a corresponding itp file with all atoms (including
hydrogens). The heavy atoms in pdb file are in sequence order as in itp
file.

e.g.
itp       pdb (no Hydrogens)
****     *****
C1       C1
H1       C2
H2       O1
H3
C2
H4
H5
O1

With this pdb (missing Hs ) Is there any way to add hydrogens (which are in
itp file) to write a *.gro file having all heavy and hydrogen atoms?

regards,
Vishal



More information about the gromacs.org_gmx-users mailing list