[gmx-users] Making covalent bonds between protein subunits

[Marc Baaden]

Dear colleagues,

I transmit the message below on behalf of my co-worker
Christoph  Meier, who is experiencing some problems with
the subscription to the mailing list.

You can reply either to the list, to me or directly to him,
I will take care that the replies reach Christoph.

Thanks in advance, and now here his actual query:



Dear all,

I am trying to setup an MD system using GROMACS 2.0:
My protein is dimeric and contains a calcium ion which interacts with both monomers.
For my simulation, I would like to introduce a virtual bond (harmonic potential) between calcium and 
specific residues of each monomer, thereby 'linking together' the monomers.

Unfortunately I haven't managed to do this so far:
I have changed the specbond.dat file, such that pdb2gmx generates bonds between the calcium and the monomers,
but when I try to use the topology file (generated by pdb2gmx) in grompp, the program crashes.
I did manage to make covalent bonds between calcium and individual subunits of the dimer (by running pdb2gmx on each individual subunits+calcium)
and use them in grompp, but I cannot put this together into one large system 
(I have tried to change the  separate topology files for the two monomers, such that they 'share' the calcium - unsuccessfully).

Has anybody ever come across such a problem ? I would be grateful for any advice !

Thanks in advance to anybody who replies,
Chris


-----------------------------------------
Christoph Meier
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3BW
U.K.
Phone  +44 1865 275380
Email  christoph.meier at hertford.ox.ac.uk
-----------------------------------------

  Marc Baaden

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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