[gmx-users] relaxing proteins gradually - how to set constraints?

[Sebastian Kruggel]

Dear gmx-users,

 

I want to relax some protein structures *gradually* using steepest descent,
first fixing everything but the hydrogens, than tethering just the backbone
and finally in a third step do the minimization of the complete structure.

In the manual / mdp-options I can only find the opposite:

> hbonds

> Convert the bonds with H-atoms to constraints.

 

I chose oplsaa-forcefield (because want to take into account druglike
molecules).

Is there another way than the mdp-file to put these constraints or do I miss
anything in general?

Thanks in advance

 

Sebastian

 

 

--

 

Sebastian Kruggel

Institut für Pharmazie

Raum 112 
Bundesstr.45 
D 20146 Hamburg

Tel. +49(0)40 42838 3626

 

-------------- next part --------------
Dear gmx-users,
 
I want to relax some protein structures *
gradually
* using steepest descent, first fixing everything but the hydrogens, than tethering just the backbone and finally in a third step do the minimization of the complete structure.
In the manual / mdp-options I can only find the opposite:
[A]
> hbonds
>
Convert the bonds with H-atoms to constraints.
 
I chose oplsaa-forcefield (because want to take into account druglike molecules).
Is there another way than the mdp-file to put these constraints or do I miss anything in general?
Thanks in advance
 
Sebastian
 
 
--
 
Sebastian Kruggel
Institut für Pharmazie
Raum 112
Bundesstr.45
D 20146 Hamburg
Tel. +49(0)40 42838 3626