[gmx-users] ligand-protein distance restraint

[Mark Abraham]

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