[gmx-users] ligand-protein distance restraint

Mark Abraham 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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