Each atom type must be in a separate group. For example: > a C17 > a C18
(and so forth for the rest of the carbon atoms in the chain) The rest of your process is fine (deleting out the other groups from the index file). -Justin Quoting ªL´µ½ <[EMAIL PROTECTED]>: > Dear all GROMACS user : > After generating the .ndx file which contained only one group that one > tail of DPPC, > I use g_order to calculate order parameters. But there are nothing in > deuter.xvg and order.xvg file. > The process is listed below: > step1: make_ndx -f XXX.pdb -o index.ndx > then type : a C17 C18 ... C31 (C31 is methyl and C17...C30 > is methylene in one tail of DPPC lipid) > then type : name 3 sn_1 (0 is for system, 1 is for DPPC, > 2 is for SOL ) > then type : q > > step2 : delete all groups in the index.ndx except sn_1 group. > > step3 : g_order -f YYY.pdb -n index.ndx -s .tpr -od > > Can someone tell me what wrong is in my process ? > > Thank you very much. ====================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://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
