Re: namdcvs Re: how to apply restraints for phi and psi for alpha helix regions

From: Leonardo Trabuco (
Date: Fri Jan 02 2009 - 02:55:40 CST

Dear Achani,

First of all, please always send questions to the mailing list.

On Tue, Dec 30, 2008 at 8:47 PM, Achani K. Yatawara
<> wrote:
> Hi Leo,
> Sorry for asking this again.
> As I mentioned in my last email,this is about namdcvs. They may be silly qustions but pls read.
> According to website I am following the following guide,
> "Bleeding-Edge (straight from CVS, requires Charm++ 6.0 or newer)
> Request and receive a username and password from us.
> Run or add the following to your login scripts (replace "username"):
> alias namdcvs 'cvs -d'
> Note that the pserver path has changed as of August 2004!
> namdcvs login (enter your password)
> In a directory that doesn't already contain a file or directory named namd2:
> namdcvs checkout namd2
> namdcvs logout "
> 1. According to this guideline, I need to have charm ++ 6.0 in order to run namd. Am I correct?
> If I successfully install charm ++6.0 Do you think that the namd2 command work well?

After you installed charmm++ 6.0, you need to install NAMD. If
everything goes well, then the namd2 command should work.

> 2. this namd2 folder containes all architectures. According to the notes given in the same folder, I need to run only for my case Linux-amd64-tcl, and ..fftw
> OR all three tcl, fftw and plugin which I saw in one problem in namd-l.

AFAIK, you need to install charmm++. fftw, tcl, and NAMD itself. If
you still have problems, your best bet is to post to namd-l the exact
steps you followed, along with any relevant information about your
system and the error you got.


> I highly apprecite your attention and time. Thank you in advance.
> Happy New year!!!
> Achani

Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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