Dear Justin, You are right, I had some warning and with -missing I override them, e.g.:
WARNING: atom HA is missing in residue HEM 105 in the pdb file WARNING: atom HB is missing in residue HEM 105 in the pdb file ... 30 missing atoms. I did not know how should figure them out. I am using GROMACS 4.5.3 and charmm27.ff. Cytochrome C is a difficult protein to simulate :( Thanks, Dariush On Tue, Jan 17, 2012 at 10:33 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Dariush Mohammadyani wrote: > >> According your help and "pdb2gmx -his -missing" I could create input >> files. Also I used grompp without error. However, for mdrun I got this >> error: >> > > Using the -missing flag is very dangerous. If you're using it to override > warnings or errors that pdb2gmx is giving, your simulations will almost > certainly be junk because the topology is broken. > > *Function type CMAP Dih. not implemented in ip_pert* >> >> >> How can I figure it out? >> >> > Without seeing your .mdp file and knowing which Gromacs version you're > using, there's little anyone can do to help you. The error suggests you're > trying to transform a CMAP dihedral using the free energy code, which > cannot be done (per the error message). > > > -Justin > > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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