VMD-L Mailing List

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Thu Jan 04 2007 - 13:02:06 CST

Thanks a lot Peter,
  I complied the source that you had sent. I first loaded the amber prmtop
file in parm7 format and then I loaded the dcd file into the molecule. To
test i just ran the following script:

set sel1 [atomselect top "resname ALA"]
namdenergy -vdw -sel $sel1 -ofile "out.dat"

First it asked me to locate namd2. I directed it to namd2.exe file on my
machine. This was namd 2.6b1.

It ended giving me the errror:

***********
namdEnergy) Using default parameter file (charmm stype):
C:/Program Files/University of
Illinois/VMD/plugins/noarch/tcl/readcharmmpar1.0/par_all27_prot_lipid_na.inp
namdEnergy) Computing energy for selection:
namdEnergy) resname ALA

namdEnergy) Running:
namdEnergy) C:/Program Files/NAMD/NAMD_2.6b1_Win32-i686/namd2.exe
namd-temp.namd

abnormal program termination

***********

The log file ended at

Reading parm file "*****.parm7".

I downloaded namd2.6 and with that the error was:

*****

namdEnergy) Using default parameter file (charmm stype):
C:/Program Files/University of
Illinois/VMD/plugins/noarch/tcl/readcharmmpar1.0/par_all27_prot_lipid_na.inp
namdEnergy) Computing energy for selection:
namdEnergy) resname ALA

namdEnergy) Running:
namdEnergy) C:/Program
Files/NAMD/NAMD_2.6_Win32-i686/NAMD_2.6_Win32-i686/namd2.exe namd-temp.namd

child process exited abnormally

******

And this time the log file was empty.

Also why is it saying that it is using default parameter charmm type? Is it
reading the amber force-field?

thanks a lot again.

Rgds,

Nitin
On 03/01/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> Dear Nitin,
> I'm attaching a recently modified version of NAMDenergy that uses amber
> files instead of charmm; please find it attached to that email; just
> source it prior to opening the namdenergy plugin during your vmd
> session. The presence of an amber-based topology is automatically
> detected. Please let me know if you have any problems. This capability
> will be included in the next release of vmd 1.8.6.
>
> I will also note that just in general, you should upgrade to vmd 1.8.5
> and namd2.6 to get the best results with this plugin.
>
> Best,
> Peter
>
> Nitin Bhardwaj wrote:
> > Dear VMD users,
> > I am trying to execute namdenergy to calculate energy with a dcd
> > file that was created with amber format input (parm 7) ".prmtop" and
> > ".inpcrd" files. But I do not know how do I specify this while running
> > namdenergy. I tried to look at the code but could not get much.
> >
> > I have VMD1.8.3 on windows platform.
> >
> > thanks a lot in advance,
> > rgds,
> > Nitin
>
>
> 

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