Re:How to fix atoms during minimization?

From: 戴伟民 (weimindai1979_at_yahoo.com.cn)
Date: Wed Nov 19 2008 - 19:52:49 CST

Hi Ghosh,

Just create a PDB file with beta set to 1 for all the protein atoms and 0 for all the water atoms. And then add the following lines to your NAMD configuration file,
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fix_backbone.pdb
fixedAtomsCol B
Substitute "fix_backbone.pdb" with your PDB file name.

Daimin Dai

--- 08年11月19日,周三, Anirban Ghosh <anirbang_at_cdac.in> 写道:
发件人: Anirban Ghosh <anirbang_at_cdac.in>
主题: namd-l: How to fix atoms during minimization?
收件人: "NAMD CGMD" <namd-l_at_ks.uiuc.edu>
日期: 2008,1119,周三,10:06下午

Hi ALL,

I want to do a minimization of my system by fixing the protein and
allowing only the water molecules to move adjust. For this what parameters
should I mention in my configuration script and with what values. Should I
use the "conskfile & conshcol" OR "fixedAtomsFile &
fixedAtomsCol" in the
script? Any suggestion is welcome. Thanks.

Regards,

-- 
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Scientific & Engineering Computing Group
Centre for Development of Advanced Computing
Pune, India
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