<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'>
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:<BR>
> > Groupname: System First atomname: C1 First atomnr 0<BR>> > Groupname: POPC First atomname: C1 First atomnr 0<BR>> > Groupname: SOL First atomname: OW First atomnr 6656<BR>> > Groupname: oleoyl First atomname: C1 First atomnr 1820<BR>> > Groupname: palmitoyl First atomname: C1 First atomnr 832<BR>> ><BR>> > Reading frame 0 time 0.000 Number of elements in first group:<BR>> > 14036<BR>> > -------------------------------------------------------<BR>> > Program g_order, VERSION 3.3<BR>> > Source code file: gmx_order.c, line: 160<BR>> ><BR>> > Fatal error:<BR>> > grp 1 does not have same number of elements as grp 1<BR>
<BR>
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.<BR>
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. <BR><BR>> Date: Sun, 3 Feb 2008 12:38:43 -0500<BR>> From: jalemkul@vt.edu<BR>> To: gmx-users@gromacs.org<BR>> Subject: Re: [gmx-users] fatal error in g_order<BR>> <BR>> <BR>> This issue is well-documented in the list archives. You need to create an index<BR>> group that specifies *only* the groups of interest in the index file, i.e. C16,<BR>> C17...<BR>> <BR>> There is a post (I believe from Dallas Warren) that even gives examples of<BR>> make_ndx commands to create such groups, if you need that kind of help.<BR>> <BR>> -Justin<BR>> <BR>> Quoting pragya chohan <pragyachohan@hotmail.com>:<BR>> <BR>> ><BR>> > hi<BR>> > I am trying to do the bilayer analysis and want to calculate order parameters<BR>> > using g_order. I made the index using make_ndx command and selected the<BR>> > carbons sai 1-16 of my first chain and 17-33 of the other in same index file<BR>> > as two separate group. When I am giving this index file to g_order I get the<BR>> > error:<BR>> ><BR>> > Using following groups:<BR>> > Groupname: System First atomname: C1 First atomnr 0<BR>> > Groupname: POPC First atomname: C1 First atomnr 0<BR>> > Groupname: SOL First atomname: OW First atomnr 6656<BR>> > Groupname: oleoyl First atomname: C1 First atomnr 1820<BR>> > Groupname: palmitoyl First atomname: C1 First atomnr 832<BR>> ><BR>> > Reading frame 0 time 0.000 Number of elements in first group:<BR>> > 14036<BR>> > -------------------------------------------------------<BR>> > Program g_order, VERSION 3.3<BR>> > Source code file: gmx_order.c, line: 160<BR>> ><BR>> > Fatal error:<BR>> > grp 1 does not have same number of elements as grp 1<BR>> ><BR>> > Please help.<BR>> ><BR>> > _________________________________________________________________<BR>> > Tried the new MSN Messenger? It’s cool! Download now.<BR>> ><BR>> http://messenger.msn.com/Download/Default.aspx?mkt=en-in_______________________________________________<BR>> > gmx-users mailing list gmx-users@gromacs.org<BR>> > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> > Please search the archive at http://www.gromacs.org/search before posting!<BR>> > Please don't post (un)subscribe requests to the list. Use the<BR>> > www interface or send it to gmx-users-request@gromacs.org.<BR>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> ><BR>> <BR>> <BR>> <BR>> ========================================<BR>> <BR>> Justin A. Lemkul<BR>> Graduate Research Assistant<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul@vt.edu | (540) 231-9080<BR>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/<BR>> <BR>> ========================================<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><BR><br /><hr />Post free auto ads on Yello Classifieds now! <a href='http://ss1.richmedia.in/recurl.asp?pid=255' target='_new'>Try it now!</a></body>
</html>