From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
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)
Enjoy!
Michel
-----Original Message-----
From: Hidekazu WATANABE [mailto:evergreen_tow_at_yahoo.co.jp]
Sent: Thursday, May 05, 2005 12:36 PM
To: namd-l_at_ks.uiuc.edu; 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
using
>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
ALAN
ATOM 2 OT1 ALA X 3 -1.019 0.921 -2.959 1.00 0.00
ALAN
ATOM 3 OT2 ALA X 3 -1.855 1.795 -4.412 1.00 0.00
ALAN
========
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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