Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations
ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.000001e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note ------------------------------------------------------- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) ------------------------------------------------------- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. Thanks in anticipation of help. Shahid Nayeem -- gmx-users mailing list gmx-users@gromacs.org http://lists.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