[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.

Bye,
Volker


> 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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: vknecht.vcf
Type: text/x-vcard
Size: 438 bytes
Desc: Card for Volker Knecht
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20011025/5741822a/attachment.vcf>


More information about the gromacs.org_gmx-users mailing list