[gmx-users] distance restraint

Anton Feenstra feenstra at chem.vu.nl
Mon Dec 1 08:51:02 CET 2003

muthu12 at cox.net wrote:

> I could be able to make distance restraint between the atoms within the proteins. How can I add distance constraint between a protein atom and a surrounding atom in a lipid. It fails when I put distance constraints in terms of atomic numbers
> Thank you
> Prabhakaran
> Is there any other way doing that other than mimicking nmr 

Retstraints between different molecules are not implemented.
There is a trick to combine protein chains into one molecule using
pdb2gmx -merge (may be called differently, check 'pdb2gmx -h').
Otherwise, you'd need to merge one (or more) lipid molecule topologies
  into your protein topology. That isn't easy, although with a script
I posted to the list (and may have put on the contributions page on
the website www.gromacs.org), it is doable:
1) label all lipid atom numbers (in atoms, bonds, angles, etc) with
    e.g. an 'L' before or after the atom numbers.
2) merge all sections separately (i.e. append lipid atoms to protein
    atoms, lipid bonds to protein bonds, etc.). You can repeat this for
    as many lipids as you may need.
3) run the 'renumtop' script on the merged topology; it will re-assign
    the right atom numbers (in atoms, bonds, angles, etc) for all lipids
    added in step 2.
4) add constraints using the new atom numbers.

Make sure in your coordinate file (.gro or .pdb), the lipids you want
to constrain come right after the protein!


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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"           |
|             | (Red Hot Chili Peppers)                               |

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