[gmx-users] energy groups

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 2 23:28:41 CET 2009 

Alright, so how about the other comment I made?  Are you using the right 
coordinate file?  I recall you got this error when you used the non-pdb2gmx 
processed .pdb file as input into grompp.  You must use the coordinate file that 
corresponds to your topology.

-Justin

Liu Shiyong wrote:
> Hi,  Justin
> I remove the del command. But I still got an error.
> 
> make_ndx -f a.pdb  -o a.ndx < make_ndx.input
> 
> make_ndx.input:
> 
> chain A and B& !a H*
> chain C& !a H*
> q
> 
> 
> 
> checking input for internal consistency...
> Opening library file /export/apps/share/gromacs/top//ffG53a6.itp
> Opening library file /export/apps/share/gromacs/top//ffG53a6nb.itp
> Opening library file /export/apps/share/gromacs/top//ffG53a6bon.itp
> Opening library file /export/apps/share/gromacs/top//ff_dum.itp
> Generated 165 of the 1596 non-bonded parameter combinations
> Opening library file /export/apps/share/gromacs/top//spc.itp
> Opening library file /export/apps/share/gromacs/top//ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 3 bonded neighbours molecule type 'Protein_B'
> Excluding 3 bonded neighbours molecule type 'Protein_C'
> 
> NOTE 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]:
>   System has non-zero total charge: -7.000002e+00
> 
> 
> 
> processing coordinates...
> double-checking input for internal consistency...
> 
> WARNING 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]:
>   With nstlist=0 atoms are only put into the box at step 0, therefore
>   drifting atoms might cause the simulation to crash.
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Making dummy/rest group for T-Coupling containing 4655 elements
> Making dummy/rest group for Acceleration containing 4655 elements
> Making dummy/rest group for Freeze containing 4655 elements
> Making dummy/rest group for Energy Mon. containing 1045 elements
> Making dummy/rest group for VCM containing 4655 elements
> Number of degrees of freedom in T-Coupling group rest is 13962.00
> Making dummy/rest group for User1 containing 4655 elements
> Making dummy/rest group for User2 containing 4655 elements
> Making dummy/rest group for XTC containing 4655 elements
> Making dummy/rest group for Or. Res. Fit containing 4655 elements
> Making dummy/rest group for QMMM containing 4655 elements
> T-Coupling       has 1 element(s): rest
> Energy Mon.      has 3 element(s): chAANDB_&_!H* chC_&_!H* rest
> Acceleration     has 1 element(s): rest
> Freeze           has 1 element(s): rest
> User1            has 1 element(s): rest
> User2            has 1 element(s): rest
> VCM              has 1 element(s): rest
> XTC              has 1 element(s): rest
> Or. Res. Fit     has 1 element(s): rest
> QMMM             has 1 element(s): rest
> Checking consistency between energy and charge groups...
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.2
> Source code file: grompp.c, line: 150
> Fatal error:
> atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in 
> different energy groups
> -------------------------------------------------------
> 
> 
> 
> On Fri, Jan 30, 2009 at 5:11 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Liu Shiyong wrote:
> 
>         -------------------------------------------------------
>         Program grompp, VERSION 4.0.2
>         Source code file: grompp.c, line: 150
> 
>         Fatal error:
>         atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are
>         in different energy groups
>         -------------------------------------------------------
> 
> 
>     Check your structure to make sure you are using the right coordinate
>     file.
> 
>     Try to *not* delete every other group in the index file.  Just
>     because you don't need these groups in your energygrps does not mean
>     they are not necessary for other functions.
> 
>     -Justin
> 
> 
>         "Can someone please tell Icarus that he's not the only one
>         falling from the sky?" (Urban Dance Squad)
> 
>                                 :-)  G  R  O  M  A  C  S  (-:
> 
>                      GROningen Mixture of Alchemy and Childrens' Stories
> 
> 
>         I checked  the a.ndx
> 
>         [ System ]
>           1    2    3    4    5    6    7    8    9   10   11   12   13
>           14   15
>          16   17   18   19   20   21   22   23   24   25   26   27   28
>           29   30
> 
>         [ chAANDB_&_!H* ]
>           1    5    6    7    8    9   10   11   12   14   15   16   17
>           18   19
>          23   24   25   26   27   28   29   30   31   32   34   35   36
>           37   38
> 
>         [ chC_&_!H* ]
>         2571 2575 2576 2577 2578 2580 2581 2582 2583 2584 2585 2586 2587
>         2588 2589
>         2590 2591 2592 2593 2594 2595 2597 2598 2599 2600 2601 2602 2605
>         2606 2607
> 
> 
> 
>         -- 
>         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
> 
> 
>         ------------------------------------------------------------------------
> 
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> 
>     -- 
>     ========================================
> 
>     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
> 
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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> (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

-- 
========================================

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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