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

From: Chris Harrison (charris5_at_nd.edu)
Date: Sun Jan 04 2009 - 12:28:23 CST

Achani,

There is a file in the namd cvs (notes.txt). It sounds like you should
read this before attempting to compile namd2+charm++ .... particularly the
section "Compiling NAMD." This will answer many of your initial questions.

C.

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Fri, Jan 2, 2009 at 2:55 AM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>wrote:
> 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
> <Achani.K.Yatawara_at_dartmouth.edu> 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 :pserver:username_at_cvs.ks.uiuc.edu:/namd/cvsroot'
> > 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.
>
> Cheers,
> Leo
>
> > 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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