VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Jun 25 2010 - 16:19:34 CDT

Namd is looking for the file
in c:\users\agyarko\Desktop\common\par_all27_prot_lipid.inp , because you
are telling it to look there in the configuration file.
You can edit the configuration file and tell it to look for the force-field
parameters in the same directory.
What I really recommend you do is:
Put namd in C:\Program Files\NAMD and add this directory to your path (
google <http://lmgtfy.com/?q=add+directory+to+path+windows&l=1> it if you
don't know how). This way you will be able to call namd2 from any folder.
Then unzip the tuturial files somewhere, for
example c:\users\agyarko\Desktop\namd_tutorial (and preserve the directory
structure!). Then (after you build the structure as in the tutorial) you can
go to c:\users\agyarko\Desktop\namd_tutorial\1-2-sphere and run the
simulation with namd2 ubq wb eq.conf > ubq wb eq.log

hope this helps,
Ajasja
On Fri, Jun 25, 2010 at 16:26, listowel agyarko <listowelagyarko_at_hotmail.com
> wrote:

> Hi Ajasja and Ramin
> I placed the needed files (parameter file, config. files, pdb and psf) in
> the namd2.exe directory. Then when I run the simulation, I get this message
> at the terminal window:
> Charm++ fatal error,
> FATAL ERROR: UNABLE TO OPEN CHARMM PARAMETER FILE
> ../common/par_all27_prot_lipid.inp
> At the terminal window, I typed dir at the prompt,
> c:\users\agyarko\Desktop\NAMD_2.7b2_win32, and confirmed that all the needed
> files (including par_all27_prot_lipid.inp) were listed. The NAMD software
> and the tutorial files were downloaded from intenet to my PC at home and I
> didn't need any account. But sometimes I am asked for rights of permission
> to do some operations on my own computer. So I don't know if this is what is
> causing that, or is it because the parameter file is simply corrupt. I tried
> to get a new parameter file from charmm website, but couldn't get the same
> as the listed one. Please I need your advice.
> Thanks
> Listowel B Agyarko
>
> ------------------------------
> Date: Wed, 23 Jun 2010 09:24:38 +0200
> Subject: Re: namd-l: Simulation configuration file not accesible
> From: ajasja.ljubetic_at_gmail.com
> To: listowelagyarko_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
>
> Hi,
>
> most probably you are not in the right directory.
> type dir to see the list of files that are in the current directory and use
> cd or prepend the relative path to the configuration file name.
> Or perhaps you do not have the right permissions (if you unpacked the
> tutorial files under a different account).
>
> Regards,
> Ajasja
>
> On Tue, Jun 22, 2010 at 22:30, listowel agyarko <
> listowelagyarko_at_hotmail.com> wrote:
>
> Hi namd users,
> I am learning Namd using the Namd tutorial manual (for windows). Each time
> I type the command "namd2 ubq_ws_eq.conf > ubq_ws_eq.log" in the terminal
> window to run the simulation, I get this message "Fatal error: Simulation
> configuration file not accesible". Could anyone help me to resolve this
> problem.
>
> Thanks
> Listowel
>
>
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