AMBER Archive (2006)

Subject: Re: AMBER: bond information in amber

From: Navnit Kumar Mishra (navnit_at_chemi.muni.cz)
Date: Fri May 12 2006 - 01:28:00 CDT

Hello;

I think you can use different atom type fo Calcium becz CA is the type
for alpha carbon.
As I know there is no bond parametrize for calcium and different
residues atom. For this you may also give a look on amber contributed
parameter link, http://pharmacy.man.ac.uk/amber/

Is it really covalent bond in your case? if not you can try to simulate
without making a bound. It will manage co-ordinate bound according to
amber force field properties.

I hope it will help you,
Navnit

snoze pa wrote:

> thanks a lot navin. I have CA, calcium atom present in my PDB. I also
> made a lib, CA.lib and try to link it with the residues in PDB file.
> The CA atom is linked to OD1 and OD2 atoms of the PDB residues. So
> when I try to link CA atom to PDB residues it is giving me
> following error message. Any help how can I fix it. The bond link
> between CYS is working fine but it is giving me error message
> while linking CA, calcium to OD1 and OD2 atoms.
> Here is the message :
> Checking for bond parameters.
> Could not find bond parameter for: O2 - CA
> No bond parameter for: O2 - CA
> Could not find bond parameter for: O2 - CA
> No bond parameter for: O2 - CA
> Could not find bond parameter for: O2 - CA
> No bond parameter for: O2 - CA
> Could not find bond parameter for: O2 - CA
> No bond parameter for: O2 - CA
> Could not find bond parameter for: O2 - CA
> No bond parameter for: O2 - CA
> Checking for angle parameters.
> Could not find angle parameter: O2 - CA - O2
> Can't find angle parameter: O2 - CA - O2
> Could not find angle parameter: O2 - CA - O2
> Can't find angle parameter: O2 - CA - O2
> Could not find angle parameter: O2 - CA - O2
> Can't find angle parameter: O2 - CA - O2
> Could not find angle parameter: O2 - CA - O2
> Can't find angle parameter: O2 - CA - O2
> Could not find angle parameter: C - O2 - CA
> Can't find angle parameter: C - O2 - CA
> Could not find angle parameter: O2 - CA - O2
> Can't find angle parameter: O2 - CA - O2
> Could not find angle parameter: O2 - CA - O2
> Can't find angle parameter: O2 - CA - O2
> Could not find angle parameter: O2 - CA - O2
> Can't find angle parameter: O2 - CA - O2
> Could not find angle parameter: O2 - CA - O2
> Can't find angle parameter: O2 - CA - O2
> Could not find angle parameter: O2 - CA - O2
> Can't find angle parameter: O2 - CA - O2
> Could not find angle parameter: C - O2 - CA
> Can't find angle parameter: C - O2 - CA
> Could not find angle parameter: C - O2 - CA
> Can't find angle parameter: C - O2 - CA
> Could not find angle parameter: O2 - CA - O2
> Can't find angle parameter: O2 - CA - O2
> Could not find angle parameter: C - O2 - CA
> Can't find angle parameter: C - O2 - CA
> Could not find angle parameter: C - O2 - CA
> Can't find angle parameter: C - O2 - CA
> There are missing parameters.
>
> thanks in advance
> snoze

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