Pathumwadee Intharathep wrote:
Dear Mark,
I tried to make a hybrid [moleculetype] section that includes one
protein and 4 ligands, it is very complicate way to do.
I have to do mannaully to put [atoms], [bonds], [pairs],
[angles] and [dihedral] for each ligand and need to re-number for all,
if not, the error of "Atoms in the .top are not numbered consecutively
from 1" will be occured.
Do you have any more esier way to make a hybrid [moleculetype] ?
No. It is fiddly, but from your starting ligand [moleculetype] you copy
and paste before adding the same integer to each atom number to generate
a ligand in the hybrid. You may find it easier to write a shell script
to do this.
There's also the advice I gave on Monday in another thread
http://www.gromacs.org/pipermail/gmx-users/2009-January/a.html
Depending how you generated your initial topologies, it may be easier to
use that tool on the whole assembly - with a force field other than ffgmx.
Mark
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