[gmx-users] Making covalent bonds between protein subunits

Volker Knecht vknecht at gwdg.de
Thu Oct 25 11:07:31 CEST 2001

Hi Chris,

an alternative solution: Instead of specifying new covalent bonds, you could define *distance restraints* on the calcium and monomer atoms (see
GROMACS manual). These are, roughly speaking, also harmonic potentials. Maybe they work better.


> 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
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