VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 16 2007 - 10:57:29 CDT

Hi,
  Before going any further, if you're using VMD 1.8.2, I would
_strongly_ recommend that you update to a current version of the program.
Much of the advice that people on the VMD-L list will give you will only
be relevant for the current versions of the program. Once you've updated
to a current version of VMD, I would suggest working your way through
the VMD tutorial here:
  http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials

After working your way through the tutorials, you'll have a MUCH better
understanding of how things work.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 16, 2007 at 10:24:21AM +0530, kinshuk_at_chem.iitb.ac.in wrote:
>
> A lot of thanks for u's consitant help.
> I have been simulating small polyalanine i.e. octaalanine peptide.I tried
> many option but i was unable to achieve it.The problem is coming in
> starting point i.e. while writing a command on vmd console, it is
> displaying the message that invalid command line (within). i also tried
> other commands like "all within 5 of residue 8". i don't know what is
> problem.Since i have been using VMD-1.8.2.Is it a installation problem or
> other like version problem.If i am trying other VMD command it is not
> accepting.I am a new VMD user plz don't mine if i am asking foolishly.
>
> > Hi Kingshuk,
> >
> > Are you simulating a regular protein, with an N-terminus and a C-terminus?
> > If not, try the foll. command:
> > "water within 5 of segname PEP"
> > where 'PEP' is whatever you have called your peptide segment. You could
> > also
> > try substituting "water" with something more specific (resname or segname,
> > for example). You need to play around until you get the right selection.
> > Keep checking your selections visually.
> > Hope this helps.
> >
> > Best,
> > Neelanjana Sengupta
> >
> > On 10/14/07, kinshuk_at_chem.iitb.ac.in <kinshuk_at_chem.iitb.ac.in> wrote:
> >>
> >> Hi all,
> >> I am student of IIT-Bombay. I have been working in the area of de
> >> novo
> >> protein designing.Now i have been working on solvation problem there i
> >> have one problem i.e. i have to select water molecule at 5 Angstrong
> >> cutt-off surrounding the peptide in simulation box.
> >> I have been exploring VMD there i came to know about command (water
> >> within 5 of protein) but when i have given the command it showd the
> >> message invalid command line (water). when i wrote within 5 0f protein
> >> it shows that invalid command line (within). i tried many times it's
> >> all command but it is not working properly.I have been using
> >> VMD-1.8.2.
> >>
> >> Please help me.
> >>
> >>
> >>
> >
> >
> > --
> > *
> >
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078