VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Oct 30 2011 - 03:28:27 CDT

Hello:
Please, I would like to learn the correct syntax in Autopsf - Add
Patch (VMD 1.9beta1, GNU-Linux) for :

PRES PLIG 0.00 ! Patch residue for Heme ligand. Residues must be,
                       ! 1-CO , 2-HEME , and 3-HIS
                       ! do NOT use AUTOgenerate ANGLes DIHEdrals
after this patch
BOND 1C 2FE
ANGLE 1C 2FE 3NE2
ANGLE 1O 1C 2FE
ANGLE 1C 2FE 2NA 1C 2FE 2NB
ANGLE 1C 2FE 2NC 1C 2FE 2ND
DIHE 1O 1C 2FE 2NA
IC 1O 1C 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1O 1C 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000

I have tried a number of (apparently wrong) combinations. All lead to
working psf/pdb files, while in no case is FE connected to the axial
histidine N and/or carbon monoxide C, as far as the pair-of-atoms in
the covalent bond section list tell. Only the four pairs of FE-N
formal bonds within the porfirin moiety appear as couples of atom IDs.

Thanks
francesco pietra