Hi Justin These errors are from bond between MET/HIS residue and Heme group of my protein. I checked for all these nine errors of bond and angle in th file ffG43a1bon.itp and I couldnt find these defined in this file. Using other options of force field also gives error at some point. waiting for your suggestion to proceed further. shahid Nayeem
On 7/15/10, Justin A. Lemkul <[email protected]> wrote: > > > shahid nayeem wrote: >> 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. >> > > That seems like a particularly poor solution. Simply getting rid of an > inconvenient group does not sound appropriate. Ask yourself whether or not > there is some functionally significant reason to having the ACE group there > (chain truncation? artificial modification?) and decide. > > As for the errors, look into the topology to see which atoms are causing the > problems. Then decide if there are indeed appropriate parameters in the > force > field for this task. > > -Justin > >> Thanks in anticipation of help. >> Shahid Nayeem > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
