<br><br><div class="gmail_quote">On Wed, Jan 28, 2009 at 6:32 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;">
<div class="Ih2E3d"><br>
<br>
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>
<br>
Thank for your helpful reply.<br>
<br>
I understand your feeling. If you have time, please see the following.<br>
<br>
mdrun has an option to output the final structure(-c). I just knew it after reading your post and checked again :<<br>
Thanks .<br>
<br>
Firstly, I run a minimized command to get the minimized structure.<br>
<br>
Secondly, based on the minimized structure, I want to do energy calculation with some user-defined energy groups. I guest I need to run second pdb2gmx.<br>
<br>
</blockquote>
<br></div>
I don't think you do. See comments below.<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The command in the Step 1:<br>
pdb2gmx -ff G53a6 -f r-l_207655_G53a6.pdb -p r-l_207655_G53a6.top -i r-l_207655_G53a6.posre.itp -o r-l_207655_G53a6.gro > r-l_207655_G53a6.output.pdb2gmx 2>&1 <br>
em.mdp<br>
<br>
title = r-l_207655_G53a6 <br>
cpp = /usr/bin/cpp <br>
define = -DFLEX_SPC <br>
constraints = none <br>
integrator = l-bfgs <br>
dt = 0.002 ; ps ! nsteps = 10000 <br>
nstlist = 20 <br>
ns_type = simple <br>
rlist = 1.8 <br>
coulombtype = shift <br>
epsilon_r = 2.0 <br>
rcoulomb = 1.8 <br>
rcoulomb-switch = 1.7 <br>
vdwtype = shift <br>
rvdw = 1.5 <br>
rvdw_switch = 1.4 <br>
</blockquote>
<br></div>
These are some bizarre cutoffs for use with 53a6, but perhaps you have your reasons...<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
pbc = no <br>
; <br>
; Energy minimizing stuff <br>
; <br>
emtol = 100.0 <br>
emstep = 0.01 <br>
<br>
grompp -f em.mdp -c r-l_207655_G53a6.gro -p r-l_207655_G53a6.top -po r-l_207655_G53a6.mdout.mdp -o r-l_207655_G53a6.input.tpr > r-l_207655_G53a6.output.grompp 2>&1 mdrun -nice 0 -v -s r-l_207655_G53a6.input.tpr -o r-l_207655_G53a6.minim_traj.trr -c r-l_207655_G53a6.minimized.pdb -e r-l_207655_G53a6.minim_ener.edr -g r-l_207655_G53a6.emlog.log > r-l_207655_G53a6.output.mdrun 2>&1<br>
<br>
Now, I get an minimized structure: r-l_207655_G53a6.minimized.pdb<br>
<br>
Then , I remove the Hydrogen atom in r-l_207655_G53a6.minimized.pdb, rename as clean2.pdb<br>
<br>
</blockquote>
<br></div>
Why are you removing hydrogens?<br>
<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>
</div></blockquote>
<br>
This is redundant. In the first pdb2gmx, you processed your structure with the 53a6 parameter set, adding some polar hydrogens and building a topology. Then, you stripped the hydrogens. Now you are adding them back. I see no point in all of these iterations.<div class="Ih2E3d">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
make_ndx -f clean2.pdb -o clean2_0.6.ndx < ./make_ndx.input > clean2_0.6.output.make_ndx 2>&1<br>
<br>
</blockquote>
<br></div>
Now you're using the original .pdb file (with no hydrogens) to make an index group. *This is where you are probably going wrong* - you are carrying out EM steps using a topology that includes H atoms on polar groups, but you are constructing index groups that correspond to a structure without H. Therefore, none of the atom numbers will correspond to what you think they are (or want them to be).<div class="Ih2E3d">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
</blockquote>
<br></div>
Again, really bizarre parameters for use with Gromos96.<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
</blockquote>
<br></div>
Right, because these two atoms were generated from a non-H structure, but you are using the .gro and .top files (with H!) as input into grompp.<br>
<br>
Here's what I'd recommend:<br>
<br>
1. Run pdb2gmx and generate your 53a6 topology.<br>
2. Make index groups from the .gro file generated by pdb2gmx.</blockquote><div><br>*.gro has no chain id information.<br>I can not make energy group(based on chain id) from *.gro file generated by pdb2gmx <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;"><br>
3. Don't strip H, just to add them back again :)</blockquote><div><br>I have the structure minimized.pdb after EM. <br><br>minimized.pdb is output from mdrun with -c option.<br><br>I tried to feed this structure into pdb2gmx. <br>
I got an error.<br><br>Processing chain 1 'A' (5360 atoms, 535 residues)<br>There are 803 donors and 760 acceptors<br>There are 1025 hydrogen bonds<br>Will use HISB for residue 212<br>Will use HISB for residue 223<br>
Will use HISB for residue 277<br>Will use HISB for residue 280<br>Will use HISB for residue 374<br>Will use HISB for residue 380<br>Will use HISB for residue 386<br>Will use HISB for residue 398<br>Will use HISB for residue 425<br>
Will use HISB for residue 440<br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 3.3.3<br>Source code file: ../../../../src/kernel/pdb2gmx.c, line: 421<br><br>Fatal error:<br>Atom HD1 in residue HISB 212 not found in rtp entry with 14 atoms<br>
while sorting atoms. Maybe different protonation state.<br> Remove this hydrogen or choose a different protonation state.<br> Option -ignh will ignore all hydrogens in the input.<br>-------------------------------------------------------<br>
<br>"You Could Be a Shadow" (The Breeders)<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;"><br>
<br>
Hopefully this makes sense.<br>
<br>
-Justin<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 class="Ih2E3d">
"God is a DJ" (Faithless)<br>
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<br>
<br>
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<br>
<br>
<br>
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<br></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>
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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">
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<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>
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<mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a>>>)<br>
<br>
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<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>
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<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>
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-- <br><div class="Ih2E3d">
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<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>