Thank you Dr. Lemkul, Could I ask one more question? Thank you! When I did the step for adding ions and minimization and equilibration steps, one warning always showed up. So I had to add -maxwarn 2 after the command gmx grompp. This warning is as follows:
WARNING 1 [file topol.top, line 48]: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Check if molecules in your system are affected by such issues before proceeding. Further information may be available at https://redmine.gromacs.org/issues/2884. It seems this warning is related to the GROMOS force field (for phosphorylation) you sent to me last week. Could I disregard this warning? Thanks! Lei On Sun, Aug 18, 2019 at 10:54 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/18/19 3:24 AM, Lei Qian wrote: > > Could I ask one more question about your *gromos43a1p.ff* force filed ? > > Thanks! > > I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce > > > > It shows a fatal error: > > "Fatal error: > > The residues in the chain xxx--xxx do not have a consistent type. The > first > > residue has type 'Protein', while residue *SEP is of type 'Other'*. > > Either there is a mistake in your chain, or it includes nonstandard > residue > > names that have not yet been added to the *residuetypes.dat file* in the > > GROMACS library directory." > > > > Then I found the *residuetypes.dat *in gromacs-2019.2/share/top, and add > > "SEP protein" to the list. > > However, the fatal error still shows up after this change. > > Could I ask how to solve this problem? > > You need to change the installed residuetypes.dat file, not the one in > the source. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
