VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jan 04 2007 - 13:05:19 CST

Hi Nitin,
could you please send me the exact input files you want to use? It may
be that I don't have it properly detecting all possible amber files --
if that's the case I'd like to fix things ;-)
Thanks,
Peter

Nitin Bhardwaj wrote:
> 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
> <mailto: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
>
>
>
>
>
> --
> $B&-(BI+I$B'*(B