Fwd: [gmx-users] Invalid atom number 6415 in indexfile
Justin A. Lemkul
jalemkul at vt.edu
Thu Jan 29 01:32:14 CET 2009
Liu Shiyong wrote:
> Hi,
>
> Thank for your helpful reply.
>
> I understand your feeling. If you have time, please see the following.
>
> mdrun has an option to output the final structure(-c). I just knew it
> after reading your post and checked again :<
> Thanks .
>
>
> Firstly, I run a minimized command to get the minimized structure.
>
> 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.
>
I don't think you do. See comments below.
> The command in the Step 1:
> 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
>
> em.mdp
>
> title =
> r-l_207655_G53a6
>
> cpp =
> /usr/bin/cpp
>
> define =
> -DFLEX_SPC
>
> constraints =
> none
>
> integrator =
> l-bfgs
>
> dt = 0.002 ; ps
> !
> nsteps =
> 10000
>
> nstlist =
> 20
>
> ns_type =
> simple
>
> rlist =
> 1.8
>
> coulombtype =
> shift
>
> epsilon_r =
> 2.0
>
> rcoulomb =
> 1.8
>
> rcoulomb-switch =
> 1.7
>
> vdwtype =
> shift
>
> rvdw =
> 1.5
>
> rvdw_switch =
> 1.4
>
These are some bizarre cutoffs for use with 53a6, but perhaps you have your
reasons...
> pbc =
> no
>
> ;
>
> ; Energy minimizing
> stuff
>
> ;
>
> emtol =
> 100.0
>
> emstep = 0.01
>
>
> 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
>
> Now, I get an minimized structure: r-l_207655_G53a6.minimized.pdb
>
> Then , I remove the Hydrogen atom in r-l_207655_G53a6.minimized.pdb,
> rename as clean2.pdb
>
Why are you removing hydrogens?
>
> *Step 2:*
> Starting structure: clean2.pdb
>
> I am trying to calculate the energy according to energy groups
>
>
> 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
>
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.
> make_ndx -f clean2.pdb -o clean2_0.6.ndx < ./make_ndx.input >
> clean2_0.6.output.make_ndx 2>&1
>
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).
> em.mdp
>
> title = clean2_0.6
> cpp = /usr/bin/cpp
> integrator = cg
> dt = 0.002 ; ps !
> nsteps = 1
> rlist = 0.55
> nstlist = 0
> vdwtype = Cut-off
> rvdw = 0.6
> coulombtype = shift
> epsilon_r = 20000
> rcoulomb = 0.6
Again, really bizarre parameters for use with Gromos96.
> rcoulomb-switch = 0.55
> energy_grps = chB chA
> ;
> ; Energy minimizing stuff
> ;
> emtol = 100.0
> emstep = 0.01
>
>
> 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
>
> Then, I got an error msg:
>
>
> clean2_0.6.output.grompp
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: ../../../../src/kernel/grompp.c, line: 307
>
> Fatal error:
> atoms 4175 and 4183 in charge group 1767 are in different energy groups
> -------------------------------------------------------
>
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.
Here's what I'd recommend:
1. Run pdb2gmx and generate your 53a6 topology.
2. Make index groups from the .gro file generated by pdb2gmx.
3. Don't strip H, just to add them back again :)
Hopefully this makes sense.
-Justin
> "God is a DJ" (Faithless)
>
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>
> On Wed, Jan 28, 2009 at 12:28 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Liu Shiyong wrote:
>
> Hi,
>
> Did you get my script ?
>
>
> As I said just a few days ago, I don't run jobs for people. I only
> have allocated time on our University's cluster, which I need for
> myself.
>
> That said, it is also very difficult to go through someone's
> scripting, laden with variables that mean nothing to anyone else but
> you, and come up with something meaningful, especially when everyone
> on this list has their own work to be doing. As I've said several
> times, simply posting your command lines with the relevant error
> message(s) is sufficient.
>
> That said, I really have no clue what you're doing with those
> scripts. It appears that you are running pdb2gmx, grompp, and
> mdrun, then using trjconv to dump out the last frame from your
> energy minimization. The last step is certainly not necessary;
> mdrun outputs the lowest-energy coordinates.
>
> Then you are running pdb2gmx again, and creating index groups. I
> don't understand the purpose of the second pdb2gmx call.
>
> The problem you are facing is easily answered with the fact that you
> simply are again using a structure file that does not have the same
> number of atoms as the structure you used to create the index file.
> It appears that your index files simply have two chains of a
> protein, with the highest atom number being 5966. So of course atom
> 6415 is missing. The simple fix is to perhaps simplify your naming
> strategy so you can keep it straight, or instead of scripting
> everything and potentially making mistakes, to just run the commands
> interactively until you have everything flowing.
>
> -Justin
>
> I dump a frame from .trr file.
> I did not define xtc-grps
>
> On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Liu Shiyong wrote:
>
> Hi,
>
> I got an error when do grompp: The input PDB file
> comes from
> the output of GROMACS by trajconv command.
>
>
> <snip>
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: ../../../../src/kernel/readir.c, line: 838
>
> *Fatal error:
> Invalid atom number 6415 in indexfile*
> -------------------------------------------------------
>
>
> Instead of screen dumps, it would be a lot more useful to see
> your
> .mdp file, as well as the command line (not output from) both
> grompp
> and trjconv. Did you dump the frame from an .xtc file? What did
> you specify in xtc-grps?
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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>
>
> --
> Shiyong Liu
> Postdoc
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu <mailto:syliu at ku.edu> <mailto:syliu at ku.edu
> <mailto:syliu at ku.edu>> (shiyongliu at ku.edu
> <mailto:shiyongliu at ku.edu> <mailto:shiyongliu at ku.edu
> <mailto:shiyongliu at ku.edu>> or liushiyong at ku.edu
> <mailto:liushiyong at ku.edu> <mailto:liushiyong at ku.edu
> <mailto:liushiyong at ku.edu>>)
>
> Homepage: http://www.people.ku.edu/~syliu
> <http://www.people.ku.edu/%7Esyliu>
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>
>
> --
> Shiyong Liu
> Postdoc
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu <mailto:syliu at ku.edu> (shiyongliu at ku.edu
> <mailto:shiyongliu at ku.edu> or liushiyong at ku.edu <mailto:liushiyong at ku.edu>)
>
> Homepage: http://www.people.ku.edu/~syliu
> <http://www.people.ku.edu/%7Esyliu>
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
>
> --
> Shiyong Liu
> Postdoc
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu <mailto:syliu at ku.edu> (shiyongliu at ku.edu
> <mailto:shiyongliu at ku.edu> or liushiyong at ku.edu <mailto:liushiyong at ku.edu>)
> Homepage: http://www.people.ku.edu/~syliu
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
> ------------------------------------------------------------------------
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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