Quoting fabracht sdf <[EMAIL PROTECTED]>: > Hello. This is my first time writing an e-mail to this list. So, please > apologize if I am doing anything wrong. > I have a basic question about gromacs. How do I restrain certain atoms in my > protein. I've tried to create an ndx file with the residues i would like to > restrain and then I created an itp file using posre. But how do I include > these restrain forces to my topology file? This path I've made, is this > correct? > Thank you >
You mean, you used genpr to create a new posre.itp file? That would be the way to go. Then just include the new posre.itp file as you would any other. Assuming you have a topol.top from pdb2gmx, look at how other topologies are included. That should tell you how to use your new .itp file. Have a thorough look through Chapter 5 of the manual for information about topologies if this is still unclear. -Justin ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
