RE: About PDB file with fixed atom flags.

From: Michel Espinoza-Fonseca (
Date: Thu May 05 2005 - 14:29:01 CDT

No, you have to say to namd the following:

fixedAtomsCol B

So, you have to change X by B. "X" is just the name of the protein, not
a big deal. (B is the column where you specify which atoms will be held
fixed during the simulation)



-----Original Message-----
From: Hidekazu WATANABE []
Sent: Thursday, May 05, 2005 12:36 PM
To:; Michel Espinoza-Fonseca
Cc: evergreen
Subject: RE: namd-l: About PDB file with fixed atom flags.

>The only thing you need is to fix some atoms, right? You can do it
>VMD and is really straightforward to do it. In the command line, after
>you load your molecule, type the following:

Thank you very much for the answer.

The character "X" is added as the fifth item in the line
which is seemd to contain the fixed atom. (Is it right?)
ATOM 1 C ALA X 3 -1.152 1.490 -3.770 1.00 0.00
ATOM 2 OT1 ALA X 3 -1.019 0.921 -2.959 1.00 0.00
ATOM 3 OT2 ALA X 3 -1.855 1.795 -4.412 1.00 0.00

Is the description about the fixed atoms in the configure file
for NAMD program followings?
(The file name with the character "X" is "solv_fix.pdb"
under the directory "ala/output/".)
fixedAtoms on
fixedAtomsFile ala/output/solv_fix.pdb
fixedAtomsCol X

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