[gmx-users] energy groups
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 3 00:26:12 CET 2009
Liu Shiyong wrote:
>
>
>
> 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.
>
"Think" is not as definite as "know" - computers are literal, so you must be, too.
>
> 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
>
Why are you running pdb2gmx twice? Unless you have multiple proteins, and need
multiple topologies, you should not be doing this.
> editconf -f a6.gro -o a6.gro -d 20.0
>
You realize that the units of -d are nm, right? Do you need such a huge
solute-box distance?
> make_ndx -f a.pdb -o a6.ndx
>
OK, here's the likely problem. If you're running pdb2gmx twice, you are
probably doing different things. So you're making an index file from a .pdb
file that was perhaps treated differently than the .gro file that corresponds to
a6.top. Use the .gro file as input into make_ndx and see if that alleviates the
problem.
> grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
>
>
This *should* work, provided the .ndx file is what you actually think it is, and
you are using the correct topology.
-Justin
>
>
> On Mon, Feb 2, 2009 at 4:28 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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>> <mailto: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>>
> <mailto: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>>
> <mailto: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> <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> <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
>
>
> --
> ========================================
>
> 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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