[gmx-users] energy groups
Liu Shiyong
liushiyong at gmail.com
Mon Feb 2 23:11:50 CET 2009
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> 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> (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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>
> --
> ========================================
>
> 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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--
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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