Follow the message that you found in the archive. The index file must specify each carbon atom type in separate groups (a group for all C12, a group for all C13, etc), and the index file must contain *only* those groups, as I told you before. If you check the output from g_order, you'll see that it is trying to involve 'System,' 'SOL,' etc. in the calculation. That should be a clue that something is going very wrong.
-Justin Quoting pragya chohan <[EMAIL PROTECTED]>: > > I had made groups using make_ndx command and selected say "a C12|a C13....." > and named one group as palmitoyl and other group as oleoyl but when I select > these groups during the execution of commamd get the error: > > > Groupname: System First atomname: C1 First atomnr 0> > Groupname: POPC > First atomname: C1 First atomnr 0> > Groupname: SOL First atomname: OW First > atomnr 6656> > Groupname: oleoyl First atomname: C1 First atomnr 1820> > > Groupname: palmitoyl First atomname: C1 First atomnr 832> >> > Reading frame > 0 time 0.000 Number of elements in first group:> > 14036> > > -------------------------------------------------------> > Program g_order, > VERSION 3.3> > Source code file: gmx_order.c, line: 160> >> > Fatal error:> > > grp 1 does not have same number of elements as grp 1 > > Is there something I am doing wrong? something I dont know of while using > g_oder. I have read the mailing list and made groups accordingly. > One more question: In the mailing list it was wriiten to make separate group > for CH3, CH2,CH. Is that the mistake I am doing since I am specifying the > whole chain. > Date: Sun, 3 Feb 2008 12:38:43 -0500> From: [EMAIL PROTECTED]> > To: [email protected]> Subject: Re: [gmx-users] fatal error in g_order> > > > This issue is well-documented in the list archives. You need to create an > index> group that specifies *only* the groups of interest in the index file, > i.e. C16,> C17...> > There is a post (I believe from Dallas Warren) that even > gives examples of> make_ndx commands to create such groups, if you need that > kind of help.> > -Justin> > Quoting pragya chohan > <[EMAIL PROTECTED]>:> > >> > hi> > I am trying to do the bilayer > analysis and want to calculate order parameters> > using g_order. I made the > index using make_ndx command and selected the> > carbons sai 1-16 of my first > chain and 17-33 of the other in same index file> > as two separate group. > When I am giving this index file to g_order I get the> > error:> >> > Using > following groups:> > Groupname: System First atomname: C1 First atomnr 0> > > Groupname: POPC First atomname: C1 First atomnr 0> > Groupname: SOL First > atomname: OW First atomnr 6656> > Groupname: oleoyl First atomname: C1 First > atomnr 1820> > Groupname: palmitoyl First atomname: C1 First atomnr 832> >> > > Reading frame 0 time 0.000 Number of elements in first group:> > 14036> > > -------------------------------------------------------> > Program g_order, > VERSION 3.3> > Source code file: gmx_order.c, line: 160> >> > Fatal error:> > > grp 1 does not have same number of elements as grp 1> >> > Please help.> >> > > _________________________________________________________________> > Tried > the new MSN Messenger? ItÂ’s cool! Download now.> >> > http://messenger.msn.com/Download/Default.aspx?mkt=en-in_______________________________________________> > > 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> >> > > > > ========================================> > 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 > _________________________________________________________________ > Post ads for free - to sell, rent or even buy.www.yello.in > http://ss1.richmedia.in/recurl.asp?pid=186 ======================================== 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
