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> 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> (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 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > > -- > ======================================== > > 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
