VMD-L Mailing List

From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Fri Sep 25 2015 - 11:11:41 CDT

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.