Dear Erik, oo.....i will be more meticulous next time. It works. :) thanks again.
Regards, bing On Thu, Jul 2, 2009 at 9:38 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > I see one typo. See below. > > Bing Bing skrev: > >> Dear all, >> I had created 3-21 group of sn1 chain for order analysis. I have issued:- >> >> make_ndx_d -f md_0_1.tpr -o sn1.dx >> > Here's the typo. You probably have an index file named sn1.dx.ndx > >> >> > a C15 >> >> Found 128 atoms with name C15 >> >> 3 C15 : 128 atoms >> >> > a C16 >> >> Found 0 atoms with name C16 >> Group is empty >> >> > a C17 >> >> Found 128 atoms with name C17 >> >> 4 C17 : 128 atoms >> >> > a C18 >> >> Found 128 atoms with name C18 >> >> 5 C18 : 128 atoms >> >> > a C19 >> >> Found 128 atoms with name C19 >> >> 6 C19 : 128 atoms >> >> > a C20 >> >> Found 128 atoms with name C20 >> >> 7 C20 : 128 atoms >> >> > a C21 >> >> Found 128 atoms with name C21 >> >> 8 C21 : 128 atoms >> >> > a C22 >> >> Found 128 atoms with name C22 >> >> 9 C22 : 128 atoms >> >> > a C23 >> >> Found 128 atoms with name C23 >> >> 10 C23 : 128 atoms >> >> > a C24 >> >> Found 128 atoms with name C24 >> >> 11 C24 : 128 atoms >> >> > a C25 >> >> Found 128 atoms with name C25 >> >> 12 C25 : 128 atoms >> >> > a C26 >> >> Found 128 atoms with name C26 >> >> 13 C26 : 128 atoms >> >> > a C27 >> >> Found 128 atoms with name C27 >> >> 14 C27 : 128 atoms >> >> > a C28 >> >> Found 128 atoms with name C28 >> >> 15 C28 : 128 atoms >> >> > a C29 >> >> Found 128 atoms with name C29 >> >> 16 C29 : 128 atoms >> >> > a C30 >> >> Found 128 atoms with name C30 >> >> 17 C30 : 128 atoms >> >> > a C30 >> >> Found 128 atoms with name C30 >> >> 18 C30 : 128 atoms >> >> > a C31 >> >> Found 128 atoms with name C31 >> >> 19 C31 : 128 atoms >> >> > a CA1 >> >> Found 128 atoms with name CA1 >> >> 20 CA1 : 128 atoms >> >> > a CA2 >> >> Found 128 atoms with name CA2 >> >> 21 CA2 : 128 atoms >> >> >del 0-2 >> >> Removed group 0 'System' >> Removed group 1 'POPC' >> Removed group 2 'SOL' >> >> Subsequently, i did this:- >> >> g_order_d -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od deuter_sn1.xvg >> >> but, i got fatal error:- >> >> Taking z axis as normal to the membrane >> Reading file md_0_1.tpr, VERSION 3.3.2 (double precision) >> 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 >> >> Reading frame 0 time 0.000 Number of elements in first group: >> 14036 >> >> ------------------------------------------------------- >> Program g_order_d, VERSION 3.3.2 >> Source code file: gmx_order.c, line: 360 >> >> Fatal error: >> grp 1 does not have same number of elements as grp 1 >> >> i have deleted the group 0-2, but why is it it still read the group 0 >> which the "system" that consist of 14036 atoms? >> >> i would be grateful of anyone can advice on this. >> >> Thanks in advance. >> >> Regards, >> bing >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Laboratory of Molecular Biophysics, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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