[gmx-users] energy groups
Liu Shiyong
liushiyong at gmail.com
Tue Feb 3 00:39:19 CET 2009
On Mon, Feb 2, 2009 at 5:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
That's because the *.gro file does not include chain id information.
If I run make_ndx -f a6.gro -o a6.ndx
I will get :
Found 0 atoms with chain identifiers A AND B
>
Found 0 atoms with chain identifier C
>
> 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?
I know the units is nm.
>
> 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>
>> <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>
>> <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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
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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