From: bo baker (bo.bybaker_at_gmail.com)
Date: Sun Oct 09 2005 - 01:52:35 CDT
Hello, NAMD:
I followed the tutorial of 'building Gramicidin A' to create a pdb
file with protein backbone atom fixed. My system contains protein,
lipids and water, namded as 'test1.pdb'. Here is how I did in VMD:
---- mol load psf test1.psf pdb test1.pdb set all [atomselect top all] set to_fix [atomselect top "protein and backbone"] $all set beta 0 $to_fix set beta 1 $all writepdb test1-fix_backbone.pdb ---- Then I read the ' test1-fix_backbone.pdb' using 'wordpad'. The file is almost identical to the oringinal one 'test1.pdb'. I wonder how NAMD could figure out the protein backone atoms are fixed based on this .pdb coordinates. Thanks for your advice Bo
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:13 CST