[gmx-users] energy groups

[Liu Shiyong]

Hi,

I tried to make energy groups based on chain id and atom type.

My purpose is to select atoms in chain A and B without Hydrogen atoms .

This is the command:

make_ndx -f a.pdb  -o a.ndx < make_ndx.input >a.log

cat make_ndx.input

del 1-9
chain A and B& !a H*
chain C& !a H*
q

And then run grompp and get an error:


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
-------------------------------------------------------

"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 (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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