From: sabri bora erdemli (serdemli_at_ku.edu.tr)
Date: Thu Mar 10 2005 - 05:36:33 CST
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
> 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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