VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Aug 04 2007 - 09:08:41 CDT

Dear Peter:
Thanks. "not resname CL3" works.

The file is named frcmod.chcl3, where atom names for carbon, chlorine, and
hydrogen are CZ, CL, HZ, in the order. There, MASS, BOND, ANGL, and NONB are
assigned.

I have now "experimented" that:

"all not type CL" removes the three chlorine atoms from all chloroform
molecules in the box. Analogously for carbon and hydrogen of the solvent with
CZ and HZ.

For the solute (a methylcyclohexane, hope you are not disappointed by the
simplicity of the trials I am carrying out) "all not type c3" or "all not type
hc" work nicely.

In summary, what remains open, is distinguishing by color chloroform from
carbon, although the "type' command shows where chlorines are.

Regards

francesco

--- Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:

> Hi Francesco,
> hiding the chloroform to see the solute should be easy enough if you
> make your graphical representation
> "not resname XXX" (where XXX is whatever residue name chloroform has in
> your system).
>
> When VMD reads a structure, it has several steps that it goes through to
> try to assign elements to each atom. The first (and most obvious) is
> that some file formats actually carry element names or numbers;
> sometimes it has to fall back to guessing based on atom name, which is
> probably what is going on here -- atoms named Csomething are being IDed
> as carbon instead of chlorine. What type of file are you reading in to
> provide the topology information for your structure? And what atom name
> do your chlorine atoms have?
>
> Best,
> Peter
>
> Francesco Pietra wrote:
> > Dealing with a chloroform box from Amber9, I was unable to hide the
> chloroform
> > molecules in order to see the solute better.
> >
> > Curiously, if I set to show carbon only, this is performed correctly for
> the
> > solute molecule, while chloroform is shown as an ammonia-like
> > umbrella with four identical atoms. I.e., chlorine is shown as if it were
> > carbon. I was unable to trace where to deal with chlorine atom.
> >
> > Thanks for help
> >
> > francesco pietra
> >
> >
> >
> >
>
____________________________________________________________________________________
> > Building a website is a piece of cake. Yahoo! Small Business gives you all
> the tools to get online.
> > http://smallbusiness.yahoo.com/webhosting
> >
>

       
____________________________________________________________________________________
Need a vacation? Get great deals
to amazing places on Yahoo! Travel.
http://travel.yahoo.com/