From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon Aug 10 2009 - 11:32:53 CDT
Please find the attached perl script to read NAMD log file. It print
the out from NAMD in a file. Plot the required parameter using gnu
plot or excel etc.
On Fri, Aug 7, 2009 at 4:45 PM, Elia Zumot<firstname.lastname@example.org> wrote:
> Dear NAMD users,
> I work with NAMD 1.8.6 on a Linux platform and have used it for SMD with
> membrane proteins. Upon using the GUI NAMD Energy to measure the
> interaction between the substrate and the protein (PME clicked, XSC and
> parameter files determined) I clicked the "Run NAMDEnergy" and got a
> message that:
> "Program not found
> Could not locate 'namd2'
> Description: NAMD 2.x Molecular Dynamics Engine
> Would you like to specify its path?"
> If I do not specify the namd file I get "Error: couldn't execute "": no
> such file or directory"
> When I do specify the namd2.exe file in \NAMD_2.7b1_Win32\, I get an error
> "Error: Processor 0 exiting: Called Cmi Abort
> Reason: FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR C NH1 CT1 C NH1
> CT1 C NH1
> Charm++ fatal error:
> FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR C NH1 CT1 C NH1 CT1 C NH1"
> I tried the same with VMD on windows XP (where everything runs normal with
> NAMD/VMD) and in this case I get a message that "Error:
> This application has requested the Runtime to terminate it in an unusual way:
> Please contact the application's support team for more information" after
> specifying the namd2.exe path.
> What should I do?
> Thanks for the help
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