RE: protein fixed in simulation

From: Ada Zhan (zyqfrog10_at_msn.com)
Date: Wed Oct 27 2010 - 18:04:55 CDT

Hi, there,

I am happen to do the similar stuff recently. The following is what I found:
1) you need 1st create a new .pdb file with B col specified as '0' for unaffected atoms, and '1' for fixed or constrained atoms. you can do it with VMD.
after you load your protein and open the TK console, type the following for example,
set all [atomselect top all]
set fixatom [atomselect top "protein"]
$all set beta 0
$fixatom set beta 1
$all writepdb fixprotein.pdb

2) then you simply implement the fix or constrain patch into your .conf file
a short example,
fixedAtoms on
fixedAtomsFile fixprotein.pdb
fixedAtomsCol B

if you want to put harmonic constraints on certain atoms, the procedure is similar. you can find more useful info. about how to select atoms in VMD guide and how to implement fix-atom and harmonic constraints patch in NAMD guide.

Good luck,
Ada

From: divya.alchemist_at_gmail.com
Date: Wed, 27 Oct 2010 11:23:56 +0530
Subject: namd-l: protein fixed in simulation
To: namd-l_at_ks.uiuc.edu

Hi,
I am doing MD simulation of a protein solvated with water. I want to ask , if i want to keep my protein fixed or flexible in simulation, what do i write in the .conf file? (which keyword)

Thanks,
Divya Nayar
                                               

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