VMD-L Mailing List

From: kinshuk_at_chem.iitb.ac.in
Date: Mon Oct 15 2007 - 23:54:21 CDT

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.
>>
>>
>>
>
>
> --
> *
>