From: John Stone (
Date: Fri Sep 25 2015 - 15:02:07 CDT

  To build structures and add missing atoms, you're best options would be to
use something like psfgen or topotools, to run molefacture, or to use
external tools and then pull the modified structure into psfgen/topotools.
While the VMD atom selectin system allows removal of structure easily,
adding is not as easy, and so that's why special purpose tools like
topotools or psfgen exist.

  John Stone

On Fri, Sep 25, 2015 at 06:11:41PM +0200, surya narayanan chandrasekaran wrote:
> Hi everyone,
> I have a system containing pyrrole like pigment for which
> i am doing QM/MM calculation for predicting excitation energy along the
> trajectory. The problem is the system don't have hydrogen on nitrogen
> according to the amber ff parametrized for it. so on truncating the pigment
> from protein and when given as XYZ coordinates for the QM calculation. The
> QM calculation crashes, because the Multiplicity is 1 apparently odd number
> of electrons. Probably the input coordinate is not recognized as resonance
> structure. So i am planning to add hydrogen to the nitrogen while going to
> the QM calculation using TCL script.
> I know how to use the truncation procedure...
> set TruncSel [atomselect top {resname XXX and name "CM[A-D]" CAA CBB CAC
> CED}]
> $TruncSel set name HHH
> $TruncSel set type HAN
> But i don't know how to add Hydrogen using TCL. Any help is appreciated.
> Note: the pigment is phycoerythrobillin so don't imagine it's only pyrrole.

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