VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Oct 30 2011 - 10:34:43 CDT
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After further managing I succeed to with autopsf to bind correctly
FE-CO, while the axial histidine binds to FE through a carbon atom.
I.e., at this step (but not before that) the protein should be
NTER/CTER prevented. Was a trick discovered withing the framework of
autopsf?
thanks
fp
On Sun, Oct 30, 2011 at 9:28 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> 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
>
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- In reply to: Francesco Pietra: "About the syntax in Autopsf - Add Patch for PRES PLIG"
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