Hi,<br><br> <br><br><div class="gmail_quote">On Wed, Jan 28, 2009 at 6:31 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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;">
Liu Shiyong wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
</blockquote>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
*Step 2:*<div class="Ih2E3d"><br>
Starting structure: clean2.pdb<br>
<br>
I am trying to calculate the energy according to energy groups<br>
<br>
<br>
pdb2gmx -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i clean2_0.6.posre.itp -o clean2_0.6.gro > clean2_0.6.output.pdb2gmx 2>&1<br>
<br>
make_ndx -f clean2.pdb -o clean2_0.6.ndx < ./make_ndx.input > clean2_0.6.output.make_ndx 2>&</div></blockquote></blockquote><div><br><br>I tried to make energy groups from the "output" (*.gro) from pdb2gmx. <br>
<br>><br>Found 0 atoms with chain identifier B<br>Group is empty<br><br>><br>Found 0 atoms with chain identifier A<br>Group is empty<br><br>That means no chain id information in *.gro, but I have to define the energy groups according to chain id .<br>
<br><br> <br><br><br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d"><br>
</div></blockquote>
So here you made some energy groups from the *input* to pdb2gmx. Make it from the *output* from pdb2gmx and you will be sure things correspond to the topology *output* from pdb2gmx. It seems rather obvious to me that your input to make_ndx has all the hydrogens still in it.<br>
<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="Wj3C7c">
em.mdp<br>
<br>
title = clean2_0.6<br>
cpp = /usr/bin/cpp<br>
integrator = cg<br>
dt = 0.002 ; ps !<br>
nsteps = 1<br>
rlist = 0.55<br>
nstlist = 0<br>
vdwtype = Cut-off<br>
rvdw = 0.6<br>
coulombtype = shift<br>
epsilon_r = 20000<br>
rcoulomb = 0.6<br>
rcoulomb-switch = 0.55<br>
energy_grps = chB chA<br>
;<br>
; Energy minimizing stuff<br>
;<br>
emtol = 100.0<br>
emstep = 0.01<br>
<br>
<br>
grompp -maxwarn 10 -f em.mdp -c clean2_0.6.gro -n clean2_0.6.ndx -p clean2_0.6.top -o clean2_0.6.input.tpr > clean2_0.6.output.grompp 2>&1<br>
<br>
Then, I got an error msg:<br>
<br>
<br>
clean2_0.6.output.grompp<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 3.3.3<br>
Source code file: ../../../../src/kernel/grompp.c, line: 307<br>
<br>
Fatal error:<br>
atoms 4175 and 4183 in charge group 1767 are in different energy groups<br>
-------------------------------------------------------<br>
<br>
"God is a DJ" (Faithless)<br>
<br>
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<br>
<br>
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<br>
<br>
<br>
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<br>
<br></div></div><div><div></div><div class="Wj3C7c">
On Wed, Jan 28, 2009 at 12:28 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Liu Shiyong wrote:<br>
<br>
Hi,<br>
<br>
Did you get my script ? <br>
<br>
As I said just a few days ago, I don't run jobs for people. I only<br>
have allocated time on our University's cluster, which I need for<br>
myself.<br>
<br>
That said, it is also very difficult to go through someone's<br>
scripting, laden with variables that mean nothing to anyone else but<br>
you, and come up with something meaningful, especially when everyone<br>
on this list has their own work to be doing. As I've said several<br>
times, simply posting your command lines with the relevant error<br>
message(s) is sufficient.<br>
<br>
That said, I really have no clue what you're doing with those<br>
scripts. It appears that you are running pdb2gmx, grompp, and<br>
mdrun, then using trjconv to dump out the last frame from your<br>
energy minimization. The last step is certainly not necessary;<br>
mdrun outputs the lowest-energy coordinates.<br>
<br>
Then you are running pdb2gmx again, and creating index groups. I<br>
don't understand the purpose of the second pdb2gmx call.<br>
<br>
The problem you are facing is easily answered with the fact that you<br>
simply are again using a structure file that does not have the same<br>
number of atoms as the structure you used to create the index file.<br>
It appears that your index files simply have two chains of a<br>
protein, with the highest atom number being 5966. So of course atom<br>
6415 is missing. The simple fix is to perhaps simplify your naming<br>
strategy so you can keep it straight, or instead of scripting<br>
everything and potentially making mistakes, to just run the commands<br>
interactively until you have everything flowing.<br>
<br>
-Justin<br>
<br>
I dump a frame from .trr file.<br>
I did not define xtc-grps<br>
On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div></div><div class="Ih2E3d">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
Liu Shiyong wrote:<br>
<br>
Hi,<br>
<br>
I got an error when do grompp: The input PDB file<br>
comes from<br>
the output of GROMACS by trajconv command.<br>
<br>
<br>
<snip><br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 3.3.3<br>
Source code file: ../../../../src/kernel/readir.c, line: 838<br>
<br>
*Fatal error:<br>
Invalid atom number 6415 in indexfile*<br>
-------------------------------------------------------<br>
<br>
<br>
Instead of screen dumps, it would be a lot more useful to see<br>
your<br>
.mdp file, as well as the command line (not output from) both<br>
grompp<br>
and trjconv. Did you dump the frame from an .xtc file? What did<br>
you specify in xtc-grps?<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="Ih2E3d">
<br>
231-9080<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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-- Shiyong Liu<br>
Postdoc<br>
center for bioinformatics in the university of kansas<br>
Lab: (785)864-1962<br></div>
Email: <a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a> <mailto:<a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a>> <mailto:<a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a><div class="Ih2E3d">
<br>
<mailto:<a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a>>> (<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a><br></div>
<mailto:<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a>> <mailto:<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a><div class="Ih2E3d"><br>
<mailto:<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a>>> or <a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a><br></div>
<mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a>> <mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a><div class="Ih2E3d"><br>
<mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a>>>)<br>
<br>
Homepage: <a href="http://www.people.ku.edu/%7Esyliu" target="_blank">http://www.people.ku.edu/~syliu</a><br></div>
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Phone: (785) 864-1962<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div><div class="Ih2E3d">
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
<br>
<br></div><div class="Ih2E3d">
-- <br>
Shiyong Liu<br>
Postdoc<br>
center for bioinformatics in the university of kansas<br>
Lab: (785)864-1962<br>
Email: <a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a> <mailto:<a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a>> (<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a> <mailto:<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a>> or <a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a> <mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a>>)<br>
<br></div>
Homepage: <a href="http://www.people.ku.edu/%7Esyliu" target="_blank">http://www.people.ku.edu/~syliu</a> <<a href="http://www.people.ku.edu/%7Esyliu" target="_blank">http://www.people.ku.edu/%7Esyliu</a>><div class="Ih2E3d">
<br>
Lab: <a href="http://vakser.bioinformatics.ku.edu/people" target="_blank">http://vakser.bioinformatics.ku.edu/people</a><br>
Phone: (785) 864-1962<br>
<br>
<br>
<br>
-- <br>
Shiyong Liu<br>
Postdoc<br>
center for bioinformatics in the university of kansas<br>
Lab: (785)864-1962<br></div><div class="Ih2E3d">
Email: <a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a> <mailto:<a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a>> (<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a> <mailto:<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a>> or <a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a> <mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a>>)<br>
Homepage: <a href="http://www.people.ku.edu/%7Esyliu" target="_blank">http://www.people.ku.edu/~syliu</a><br>
Lab: <a href="http://vakser.bioinformatics.ku.edu/people" target="_blank">http://vakser.bioinformatics.ku.edu/people</a><br>
Phone: (785) 864-1962<br>
<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Shiyong Liu<br>Postdoc<br>center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone:         (785) 864-1962<br>