Tutorial-l Mailing List

From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Apr 17 2012 - 19:23:54 CDT

I forgot to copy tutorial-l_at_ks.uiuc.edu on this email. Forwarding for
posterity.

---------- Forwarded message ----------
From: Chris Harrison <charris5_at_gmail.com>
Date: Tue, Apr 17, 2012 at 7:22 PM
Subject: Re: help
To: rohit <rclappa_at_gmail.com>

Do ANY of the directory names in the path to either namd or the config
file(s) contain ANY spaces? If so, try moving to a directory path that
doesn't contain spaces.

And namd is executed by passing it the config file name, ie "namd2
yourConfileFile.conf"

Remember to include the "2" at the end of namd, as "namd2" is the proper
name of the namd binary.

Regarding vmd and generating your psf, you should begin by checking that
vmd is acting in the same working directory as you expect. Try typing
"pwd" in the tkconsole to see if you are in the directory you expect.

Best,
Chris

On Tue, Apr 17, 2012 at 1:59 AM, rohit <rclappa_at_gmail.com> wrote:

> Respected sir,
>
> Actually sir what additional softwares needed to be installed to run namd
> in w7 os.
> I have cygwin (default version), charm++ (6.2.1),Gnu tools, vmd.
>
> actually I have unziped win32 namd multicore and saved at
> c:>programefiles(x86)>namd
> and tried to execute namd.exe, it has given the fatal error no config file.
>
> I have followed the tutorial but facing problem with generating psf file
> through vmd tkconsole.
> the directory 1-1-build was open in terminal window (cmd), and I tried to
> generate ubqp.pdb
> in the dir 1-1-build but ubqp.pdb was not generated even though in the vmd
> window it is giving
> finished writing to ubqp.pdb.
>
> kindly help me in this regard.
>
>
> thanking you,
>
>
>
>
>
>
>
>
>
>
>
> _
>
> Rohit Chilappa
> M.S (Pharm)
> NIPER-Hyderabad
>
>
>
> On 16 April 2012 18:39, Chris Harrison <charris5_at_gmail.com> wrote:
>
>> Dear Rohit,
>>
>> You are likely missing the input config file. You should work
>> through the namd tutorial to learn how to use the software.
>>
>>
>> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/index.html
>>
>> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files.zip
>>
>> Best,
>> Chris
>>
>> On Mon, Apr 16, 2012 at 8:06 AM, Diane Davis <ddavis5_at_ks.uiuc.edu> wrote:
>> >
>> > Could someone please respond to the person in this email.
>> > Thanks,
>> > Diane
>> >
>> > -------- Original Message --------
>> > Subject: help
>> > Date: Sun, 15 Apr 2012 17:09:29 +0530
>> > From: rohit <rclappa_at_gmail.com>
>> > To: ddavis5_at_ks.uiuc.edu, kschulte_at_ks.uiuc.edu, zan_at_ks.uiuc.edu
>> >
>> >
>> >
>> > Respected sir,
>> >
>> > sir, I have tried to install NAMD on my windows 7 os.
>> > while I have executed namd2.exe file it is giving error
>> > "Fatal error: no config file on command line"
>> > I am unable to install it, kindly help me in this
>> > regard.
>> >
>> > thanking you,
>> >
>> > Rohit Chilappa
>> > M.S (Pharm)
>> > NIPER-Hyderabad
>> >
>> >
>>
>>
>>
>> --
>> Chris Harrison, Ph.D.
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Theoretical and Computational Biophysics Group
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>>
>> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
>> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>>
>
> 

-- 
Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
http://www.ks.uiuc.edu/Research/namd       Voice: 773-570-6078
http://www.ks.uiuc.edu/~char                          Fax: 217-244-6078
-- 
Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
http://www.ks.uiuc.edu/Research/namd       Voice: 773-570-6078
http://www.ks.uiuc.edu/~char                          Fax: 217-244-6078
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