Re: restraining residues in NAMD

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Wed Sep 28 2011 - 19:44:34 CDT

Hi Haydee,

Have a look at:
http://www.ks.uiuc.edu/Research/namd/2.8/ug/node27.html#SECTION00085300000000000000
and the SMD section of the NAMD tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node17.html
which will show you how to fix one atom, from which you can
extrapolate how to fix the rest.

cheers,
Johan

------------------------------------------------------------------------------------------------------
Johan Strumpfer:         johanstr_at_ks.uiuc.edu        www.ks.uiuc.edu/~johanstr
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
------------------------------------------------------------------------------------------------------

On Thu, Sep 29, 2011 at 12:32 AM, flavio seixas <oivalf_nix_at_yahoo.com> wrote:
> Hi
>
> Use nedit software. It is a column editor. You may select the column of 0.00 values and using the replace tabe of the editor, change them to 1.00
>
> regards
>
> flavio
>
> --- On Wed, 9/28/11, Haydee Valdes <hvaldesg10_at_gmail.com> wrote:
>
>> From: Haydee Valdes <hvaldesg10_at_gmail.com>
>> Subject: namd-l: restraining residues in NAMD
>> To: namd-l_at_ks.uiuc.edu
>> Date: Wednesday, September 28, 2011, 4:59 PM
>> Good afternoon,
>> my problem is very simple. I have a pdb file containing a
>> solvated protein.
>>
>> I would like to fix the atoms/residues of the protein and
>> simply
>> adjust the waters around it.
>> I haven´t found an easy way to do that in NAMD though.
>>
>> Is there a way to specify the following:  fix from
>> atom/residue X to
>> atom/residue Y and move everything else?
>>
>> Thnx
>>
>> hyd
>>
>>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:47 CST