Dear Erik,<br>oo.....i will be more meticulous next time.<br>It works. :)<br>thanks again.<br><br>Regards,<br>bing<br><br><div class="gmail_quote">On Thu, Jul 2, 2009 at 9:38 PM, Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I see one typo. See below.<br>
<br>
Bing Bing skrev:<div class="im"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear all,<br>
I had created 3-21 group of sn1 chain for order analysis. I have issued:-<br>
<br>
make_ndx_d -f md_0_1.tpr -o sn1.dx<br>
</blockquote></div>
Here's the typo. You probably have an index file named sn1.dx.ndx<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
<br>
> a C15<br>
<br>
Found 128 atoms with name C15<br>
<br>
3 C15 : 128 atoms<br>
<br>
> a C16<br>
<br>
Found 0 atoms with name C16<br>
Group is empty<br>
<br>
> a C17<br>
<br>
Found 128 atoms with name C17<br>
<br>
4 C17 : 128 atoms<br>
<br>
> a C18<br>
<br>
Found 128 atoms with name C18<br>
<br>
5 C18 : 128 atoms<br>
<br>
> a C19<br>
<br>
Found 128 atoms with name C19<br>
<br>
6 C19 : 128 atoms<br>
<br>
> a C20<br>
<br>
Found 128 atoms with name C20<br>
<br>
7 C20 : 128 atoms<br>
<br>
> a C21<br>
<br>
Found 128 atoms with name C21<br>
<br>
8 C21 : 128 atoms<br>
<br>
> a C22<br>
<br>
Found 128 atoms with name C22<br>
<br>
9 C22 : 128 atoms<br>
<br>
> a C23<br>
<br>
Found 128 atoms with name C23<br>
<br>
10 C23 : 128 atoms<br>
<br>
> a C24<br>
<br>
Found 128 atoms with name C24<br>
<br>
11 C24 : 128 atoms<br>
<br>
> a C25<br>
<br>
Found 128 atoms with name C25<br>
<br>
12 C25 : 128 atoms<br>
<br>
> a C26<br>
<br>
Found 128 atoms with name C26<br>
<br>
13 C26 : 128 atoms<br>
<br>
> a C27<br>
<br>
Found 128 atoms with name C27<br>
<br>
14 C27 : 128 atoms<br>
<br>
> a C28<br>
<br>
Found 128 atoms with name C28<br>
<br>
15 C28 : 128 atoms<br>
<br>
> a C29<br>
<br>
Found 128 atoms with name C29<br>
<br>
16 C29 : 128 atoms<br>
<br>
> a C30<br>
<br>
Found 128 atoms with name C30<br>
<br>
17 C30 : 128 atoms<br>
<br>
> a C30<br>
<br>
Found 128 atoms with name C30<br>
<br>
18 C30 : 128 atoms<br>
<br>
> a C31<br>
<br>
Found 128 atoms with name C31<br>
<br>
19 C31 : 128 atoms<br>
<br>
> a CA1<br>
<br>
Found 128 atoms with name CA1<br>
<br>
20 CA1 : 128 atoms<br>
<br>
> a CA2<br>
<br>
Found 128 atoms with name CA2<br>
<br>
21 CA2 : 128 atoms<br>
<br>
>del 0-2<br>
<br>
Removed group 0 'System'<br>
Removed group 1 'POPC'<br>
Removed group 2 'SOL'<br>
<br>
Subsequently, i did this:-<br>
<br>
g_order_d -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od deuter_sn1.xvg<br>
<br>
but, i got fatal error:-<br>
<br>
Taking z axis as normal to the membrane<br>
Reading file md_0_1.tpr, VERSION 3.3.2 (double precision)<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>
<br>
Reading frame 0 time 0.000 Number of elements in first group: 14036<br>
<br>
-------------------------------------------------------<br>
Program g_order_d, VERSION 3.3.2<br>
Source code file: gmx_order.c, line: 360<br>
<br>
Fatal error:<br>
grp 1 does not have same number of elements as grp 1<br>
<br>
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?<br>
<br>
i would be grateful of anyone can advice on this.<br>
<br>
Thanks in advance.<br>
<br>
Regards,<br>
bing<br>
<br>
<br>
<br></div></div>
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</blockquote>
<br>
<br>
-- <br>
-----------------------------------------------<br>
Erik Marklund, PhD student<br>
Laboratory of Molecular Biophysics,<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 4537 fax: +46 18 511 755<br>
<a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a href="http://xray.bmc.uu.se/molbiophys" target="_blank">http://xray.bmc.uu.se/molbiophys</a><br>
<br>
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</blockquote></div><br>