Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Liu Shiyong liushiyong at gmail.com
Thu Jan 29 17:45:48 CET 2009


Hi,



On Wed, Jan 28, 2009 at 6:31 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> Liu Shiyong wrote:
>
>> Hi,
>>
>
>
>> *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
>>
>> make_ndx -f clean2.pdb  -o clean2_0.6.ndx < ./make_ndx.input >
>> clean2_0.6.output.make_ndx 2>&
>>
>

I tried to make energy groups from the "output" (*.gro)  from pdb2gmx.

>
Found 0 atoms with chain identifier B
Group is empty

>
Found 0 atoms with chain identifier A
Group is empty

That means no chain id  information in *.gro,  but I  have to define the
energy groups according to chain id .







>
>>  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.
>
>  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
>> 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
>> -------------------------------------------------------
>>
>> "God is a DJ" (Faithless)
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 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>
>>        <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><
>> 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<http://www.people.ku.edu/%7Esyliu>
>> Lab:    http://vakser.bioinformatics.ku.edu/people
>> Phone:      (785) 864-1962
>>
>>
>> ------------------------------------------------------------------------
>>
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-- 
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or 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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