VMD-L Mailing List

From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Fri Sep 25 2015 - 15:34:23 CDT

hi okay,

I just want to add a dummy H atom while translating the trakectory XYZ
coordinates to QM calculation. Let me know if there is any possiblities. is
there a way to use the reduce command in the TCL script?

Note: Probably this might be a future possiblity for VMD to include the
atoms to respective position.

thanks
Surya

On Fri, Sep 25, 2015 at 10:02 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> 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.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> 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.
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
> 

-- 
Suryanarayanan C
M.S Chemist
01742857830