[gmx-users] pdb2gmx does create bonds b/w DNA bases!

Azazel S'irim azizelo at yahoo.com
Tue Nov 18 00:04:01 CET 2003


I'm trying to do MD on a dsDNA dodecamer.  After
spending two days on this, I finally figured out why
grompp crashes.  It appears that pdb2gmx does not
create the bond between the individual DNA
nucleotides.  There is no bond connecting the O3' of
the n-1 residue with the P of residue n.  And because
of this no dihedral values are written for the
corresponding dihedral angle and that makes pdb2gmx
crash.  Any suggestions!?  Where is the info for
'linking' residues contained?  I'm using GROMOS96
(official distribution) forcefield.  Thanks

Tinoush Moulaei
School of Chemistry and Biochemistry
Georgia Institute of Technology

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