On Mon, Feb 2, 2009 at 5:26 PM, Justin A. Lemkul <jalem...@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 <jalem...@vt.edu<mailto: >> jalem...@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 >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@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: sy...@ku.edu <mailto:sy...@ku.edu> >> <mailto:sy...@ku.edu <mailto:sy...@ku.edu>> <mailto:sy...@ku.edu >> <mailto:sy...@ku.edu> >> >> <mailto:sy...@ku.edu <mailto:sy...@ku.edu>>> >> (shiyong...@ku.edu <mailto:shiyong...@ku.edu> >> <mailto:shiyong...@ku.edu <mailto:shiyong...@ku.edu>> >> <mailto:shiyong...@ku.edu <mailto:shiyong...@ku.edu> >> >> <mailto:shiyong...@ku.edu <mailto:shiyong...@ku.edu>>> or >> liushiy...@ku.edu <mailto:liushiy...@ku.edu> >> <mailto:liushiy...@ku.edu <mailto:liushiy...@ku.edu>> >> <mailto:liushiy...@ku.edu <mailto:liushiy...@ku.edu> >> >> <mailto:liushiy...@ku.edu <mailto:liushiy...@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 >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@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-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> 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 >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@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: sy...@ku.edu <mailto:sy...@ku.edu> <mailto:sy...@ku.edu >> <mailto:sy...@ku.edu>> (shiyong...@ku.edu >> <mailto:shiyong...@ku.edu> <mailto:shiyong...@ku.edu >> <mailto:shiyong...@ku.edu>> or liushiy...@ku.edu >> <mailto:liushiy...@ku.edu> <mailto:liushiy...@ku.edu >> <mailto:liushiy...@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@gromacs.org >> <mailto:gmx-users@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-requ...@gromacs.org >> <mailto:gmx-users-requ...@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: sy...@ku.edu <mailto:sy...@ku.edu> (shiyong...@ku.edu <mailto: >> shiyong...@ku.edu> or liushiy...@ku.edu <mailto:liushiy...@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@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-requ...@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: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962
_______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
