From: Rebecca Swett (rswett_at_chem.wayne.edu)
Date: Fri Apr 05 2013 - 09:23:54 CDT
Hey, to write the text index file, you can open the file in VMD, and
then use the following script in the TK console substituting in whatever
index name and atom selection you want to fix.
set sel1 [atomselect top "selection"]
set f [open "indexfile.txt" w+]
set index [$sel1 get index]
puts $f $index
close $f
Open the structure pdb that you'll be using for the simulation, not a
pdb subset. We want the correct indices relative to the whole simulation
and depending on how you generated that pdb, your atoms may be
renumbered. Substitute "selection" with the atomselection for whatever
you want to hold fixed. Same for "indexfile.txt" use whatever name you
want. If you're going to be doing a lot of simulations, I suggest just
going through the TK tutorial. It makes these sorts of things much
easier and faster.
Rebecca Swett
Wayne State University
357 Chemistry
Detroit, MI 48201
Lab Phone 313-577-0552
Cell Phone 906-235-0768
On 4/5/2013 1:25 AM, Ramya Gamini wrote:
> Hi Sridhar,
>
> "The text input file for fixed atoms is not found!"
>
> The fixed atom file here should be a "text file" of indices/ indexes
> for the atoms you want fixed and *not a PDB file*
>
> best,
> Ramya
> TCBG, UIUC
>
>
> On Thu, Apr 4, 2013 at 9:33 PM, Sridhar Kumar Kannam
> <srisriphy_at_gmail.com <mailto:srisriphy_at_gmail.com>> wrote:
>
> Dear NAMD users,
>
> I am using memory optimized NAMD version as my system has several
> million atoms.
> I followed the instruction on this page -
> http://www.ks.uiuc.edu/Research/namd/wiki/?NamdMemoryReduction
> and did everything fine.
>
> With the compressed psf file and, binary coordinate file the
> simulations are running fine.
>
> But when I include a fixedatoms.pdb file in the configuration file
> I am getting the error - FATAL ERROR: The text input file for
> fixed atoms is not found!
> But the fixed atoms file is there in the directory.
>
> When we use memory optimized version, is anything should be
> changed regarding the fixedatoms file ?
>
> Thanks for any suggestion ....
>
> --
> Cheers !!!
> Sridhar Kumar Kannam :)
>
>
>
>
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