From: Chris Harrison (charris5_at_gmail.com)
Date: Sun Oct 31 2010 - 08:23:46 CDT
Dear Catherine,
Use VMD. Load the coordinate (pdb or coor) file used in your namd config.
From the extensions menu, open the TkCon window. Then (replacing text
between < > symbols with your desired values):
set allAtomsSel [atomselect top all]
$allAtomsSel set occupancy 0
set tcoupledAtomSel [atomselect top "<YOUR SELECTION TEXT FOR TEMP COUPLED
ATOMS>"]
$tcoupledAtomSel set occupancy <TEMP TO WHICH ATOMS SHOULD BE COUPLED>
$allAtomsSel writepdb tCoupledFile.pdb
Best,
Chris
2010/10/29 a a <patd_2_at_hotmail.com>
> Dear Sir/Madam,
>
> How to generate the tCouple file? e.g. if we need the following line in
> our configuration file.
>
>
> #tCoupleFile $fname.tCouple.pdb ### friction coef.=1.0
>
> What is the best way to generate the pdb file?
>
> Best regards,
>
> Catherine
>
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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