[gmx-users] Distorted bonds

Chris Gaughan clgaughan68 at yahoo.com
Tue Sep 27 07:28:25 CEST 2005


I have placed two 28 aa acid alpha helices next to
each other (~ 2nm apart). When I run the energy
minimization, some of the bonds become extremely long
and distorted. I have read other posts where a similar
thing has happened with phosphate groups becoming
distorted after em. It seems one person solved the
problem by using protonated phospahates. It seems this
has also happened in DNA/RNA simulations. Here again,
missing hydrogens were a problem.

I use the -ignh option in pdb2gmx. Is this causing my
problems? Or do I need to use dummy atoms? My peptides
do have some aromatic residues.


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