[gmx-users] Tethering

[Anton Feenstra]

David van der Spoel wrote:

> On Fri, 6 May 2005, Joanne Hanna wrote:
> 
> 
>>Hi
>>
>>Thank you, I had misunderstood what the purpose of the position restraints file. If I have a protein posre.itp and ligand posre.ipt files do i leave them all as seperate files of the same name or do I combine then, also where do i define the force constant and if i have had to make a topology file (which I have had to for an AMP ligand) how do i generate a position restraints file for this?
> 
> there is a utility called genpr

Position restrains, in Gromacs, are a property of a certain molecule 
type, e.g. your protein or the AMP. Each of molecules that you want to 
restrain, will need its own [position_restraints] section. This you 
could add (manually) to the molecule's .top or .itp file, but more 
commonly it is included into the respective file by an '#include' 
statement, like:

-- file protein.top --

[defaults]
...

[moleculetype]
protein ...
[atoms]
...
...

#ifdef POSRE
#include posre.itp
#endit

#include AMP.itp
--- end of file protein.top --

And the AMP.itp would look like:
[moleculetype]
AMP ...
[atoms]
...
...
#ifdef POSRE
#include posre_AMP.itp
#endif

The posre*.itp file would look like
[position_restraints]
1 1 200
2 1 200
3 1 200
...

Where 1, 2, 3 are the atom numbers to be restrained, i.e. one for each 
atom in your molecule. This may be hundreds or thousands for your 
protein, and several tens for your AMP. Indeed, for this part there is a 
tool called 'genpr' which acccepts an index file and will write a posre 
file for one index group (set of atoms).



-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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