I think you may want to use an NMR restraint style rather than literal
bonds, since bonds would force you to develop unusual dihedral and angle
force field terms. E.g. if an ion is 4A from an atom, you could add a
restraint that started at 5A (making up numbers).
It's worth checking the literature to see what other people did in
comparable situations.
I'm not sure 'coordinate bond' means anything?
Bill
On 10/16/20 9:53 PM, Jenny 148 wrote:
> Hi,
> I have a pdb structure, where in I have added a few zinc ions. These zinc
> ions are supposed to be coordinated with a few of the Amino acids. Since I
> added the ions by simple superimposition, the coordinate bond is not well
> defined and the ions are far from the expected position. Is there some way
> to change the position of these ions in xleap and create the coordinate
> bond required in this system? Thank you in advance.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Phobrain.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 16 2020 - 22:30:02 PDT
