Hi, Mark, I tried your suggestion.
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb + editconf -f a6.pdb -o a6.gro -d 20.0 + make_ndx -f a6.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr title = b cpp = /usr/bin/cpp integrator = cg dt = 0.002 ; ps ! nsteps = 1 rlist = 0.55 nstlist = 0 vdwtype = Cut-off rvdw = 0.6 coulombtype = Cut-off epsilon_r = 2 rcoulomb = 0.6 energy_grps = chAANDB_&_!H* chC_&_!H* ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.01 I got the same error. ------------------------------------------------------- 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 ------------------------------------------------------- "It's Against the Rules" (Pulp Fiction) On Mon, Feb 2, 2009 at 7:05 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > > Liu Shiyong wrote: >> >> 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 > > > I think you still don't need two invocations of pdb2gmx. Your only constraint > is that you want chain IDs preserved for your make_ndx command. The PDB > format carries the system size just like the GRO format. Thus > > + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb > + editconf -f a6.pdb -o a6.gro -d 20.0 > + make_ndx -f a6.pdb -o a6.ndx > > + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr > > Simpler still is to define your index groups using information other than the > chain ID - as I think someone suggested days ago. Ranges of atom numbers are > also effective. > > >> ------------------------------------------------------- >> 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 >> >> ------------------------------------------------------- >> >> >> There is still some sort of disconnect between topology numbering >> (which is where charge groups are defined), and the structure you >> are using. Can you post the first *few* lines of your .pdb file, [ >> atoms ] section of the .top, and the relevant index groups? > > > Not necessarily - the assignment of energy groups in the .mdp file is still a > potential source of problems. > > Mark > > _______________________________________________ > 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
