[gmx-users] peptide translation
priyankaps4 at yahoo.com
Wed Aug 6 21:31:25 CEST 2008
I have a lipid - peptide system and while running the production run I forgot to assign comm-grps, thus the peptide has actually shifted from the center towards one of the edges. I have searched the forum and tried all possible options in trjconv i.e. -center zero, -fit translation, progressive etc. but mostly the entire bilayer shifts but the peptide does not move from its place. I am selecting the "Protein" option from trjconv when it asks for "group used for centering"
How to translate the peptide only in a lipid-peptide system to a certain point? This is a short peptide in the top layer of the lipid bilayer and my bilayer center is at (0,0,0). I want to put the peptide at (0,0,1.7). I even tried using the shift option, but that does some weird things.
Searching forum results in centering peptide in a water box i.e. peptide or protein at 0,0,0 and also mainly the threads that are already there talks about using trjconv center and translation options! I really apologize if I missed out any thread related to this and shall be really grateful if experts out there would kindly help me out.
eagerly waiting for the response,
Be the first one to try the new Messenger 9 Beta! Go to http://in.messenger.yahoo.com/win/
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users