From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Thu Mar 10 2005 - 07:59:14 CST
In what residue do you see the CT2-CP2 bond? Could you post the part of the
PSF file that describes that residue?
On Thursday 10 March 2005 12:36, sabri bora erdemli wrote:
> as you said this bond should not be in the structure. However; we saw this
> bond in the psf file which is generated by psfgen. I used top27 CHARMM
> topology file and I use it for all my past simulations. I have faced with
> the same problem before but I could not solve it I just changed the
> structure with an homolog one.
> Do you have any further suggestion?
> > Fatal error on PE 0> FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND
> CP2 -
> > CT2 IN PARAMETER FILES
> > When I tried to find the bond CP2 - CT2, I saw that this was not an usual
> > bond. In the pdb file there is no ligand or any other chemical compound.
> > There is only protein complex.
> CP2 carbon atoms should only exist in proline sidechains, where they should
> not be linked to a CT2 carbon. I suggest you look for atoms of type CP2 in
> your PSF file, and see in what context they are. You may also check that
> you have no CT2 atoms in proline sidechains. If there are, check your
> topology file for the corresponding residue.
-- Jérôme Hénin Equipe de Dynamique des Assemblages Membranaires Université Henri Poincaré / CNRS Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71 http://www.edam.uhp-nancy.fr/
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