VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Sun Oct 14 2007 - 08:05:40 CDT

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.
>
>
> 

-- 
*