Re: Fixing atoms during simulation

Date: Sat May 07 2005 - 23:17:30 CDT

Dear Uma (and others who may be confused) --

Here is what you need to do:

- First, create a modified PDB file, in which you specify which atoms
are going to be held fixed and which are not; you do this by choosing
a column in the PDB file (either the X, Y, Z, O, or B column) and then
re-writing the value in that column, so that it has the value "1.0"
for the atoms to be fixed and the value "0.0" for all the other atoms.
(In this way, the column you choose acts as a "flag" for NAMD to see which
atoms you want to be fixed.)

- Next, create your NAMD configuration file, and just make sure that the
"fixedAtomsCol" parameter agrees with the name of the column you chose
to use as a flag, and the "fixedAtomsFile" parameter has the PDB filename.

The common confusion is that X,Y,Z,O,B, are the *names* of the columns,
not the values that you need to put into those columns.

Hope this helps!

- Erik

C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

Quoting Uma Mahankali <>:

> Hello,
> I read through the posts regarding the fixingatoms option but it still
> doesn't work for me.
> I have a pdb file with the fifth column X for just the protein part
> and this is what I have in my configuration file:
> fixedAtoms on
> fixedAtomsFile src/solv3_box_namd_fixed.pdb
> fixedAtomsCol X
> However, when I do this and run a short minimization, ALL of the
> structure is fixed. I have all the coordinates from the original pdb
> file in the fixed pdb with just the added 'X' in the fifth column for
> the atoms to be fixed.
> I just moved from Charmm to NAMD and I am lost..
> Could someone help me out please?
> Thanks,
> Uma Mahankali

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