[gmx-users] energy groups

Liu Shiyong liushiyong at gmail.com
Tue Feb 3 00:21:52 CET 2009 

pdb2gmx  -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p
r-l_365130_G53a6.minim_traj_withH_0.6.top -i
r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o
r-l_365130_G53a6.minim_traj_withH_0.6.gro
>r-l_365130_G53a6.minim_traj_withH_0.6.output.pdb2gmx 2>&1

Hi, Justin



grompp read the coordinate file : a6.gro from the output of editconf.
editconf read the  a6.gro ( output from the first pdb2gmx).

top file a6.top from the output of  the first pdb2gmx.

I think the the coordinate file  corresponds to the topology file a6.top.


Here is my command.

 pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro

 pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb

 editconf -f a6.gro -o a6.gro -d 20.0

 make_ndx -f a.pdb -o a6.ndx

 grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr




On Mon, Feb 2, 2009 at 4:28 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
> 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>
>>        <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
>>
>>    ========================================
>>    _______________________________________________
>>    gmx-users mailing list    gmx-users at gromacs.org
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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<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 | (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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