[gmx-users] fatal error in g_order

[pragya chohan]

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: jalemkul at vt.edu> To: gmx-users at gromacs.org> 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 <pragyachohan at hotmail.com>:> > >> > 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? It’s cool! Download now.> >> http://messenger.msn.com/Download/Default.aspx?mkt=en-in_______________________________________________> > gmx-users mailing list gmx-users at gromacs.org> > 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 gmx-users-request at gromacs.org.> > 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> jalemkul at vt.edu | (540) 231-9080> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > ========================================> _______________________________________________> gmx-users mailing list gmx-users at gromacs.org> 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 gmx-users-request at gromacs.org.> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080204/0b7e1bc5/attachment.html>