[gmx-users] energy groups

[Justin A. Lemkul]

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> (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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