[gmx-developers] distance restraints between protein and ligand

[Anton Feenstra]

Hi,


Following up on the gmx-users question from Chris de Graaf (in my group),
I was wondering how the defenitions are for creating 'shake-blocks'. As
I see it, now they are created based on 'connects', which are normally
associated with bonds (or constraints). But, as in the case of protein
plus ligand with distance restraints, the protein and ligand should be
considered as one shake-block, at least with respect to the PBC. Is there
a reason (other than 'historical') to have shake blocks depend on connects,
and not on any type of bonded interaction (which includes disre)?

There is a problem associated with adding a 'manual' connect (bond type 5)
between protein and ligand, as this also invokes additional exclusions (as
per 'nrexcl') between ligand and protein. The impact of this can be minimized
by taking a protein atom far away from the ligand, but it would be nice to
have a real solution.

P.S., the same goes of course for any restraint to be placed between two
separate molecules, like two protein monomers in a dimer.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
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