[gmx-users] ligand-protein distance restraint
Mark.Abraham at anu.edu.au
Tue Jan 27 22:23:11 CET 2009
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
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.
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