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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>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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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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