Hello, I believe this question has been asked several times. It is true that ffoplsaabon.itp misses some parameters for dihedral for the capped residues (ACE NAC). I think you can add some estimated values to the ffoplsaabon.itp, or ignore the warnings.
All the best! Donnsheng On Sat, 2006-09-02 at 14:36 +0200, singh wrote: > > > > Hi, > I have checked both the files. These lines corresponds to following > dihedrals in my topology > > Dihedral (1-5-7-9) > 1 opls_135 1 ACE CH3 1 -0.18 12.011 ; qtot > -0.18 > 5 opls_235 1 ACE C 2 0.5 12.011 ; qtot > 0.5 > 7 opls_238 2 PHE N 3 -0.5 14.0067 ; qtot > -0.5 > 9 opls_224B 2 PHE CA 3 0.14 12.011 ; qtot > -0.06 > > And (81-88-90-92) > 81 opls_224B 6 SER CA 30 0.14 12.011 ; > qtot -0.06 > 88 opls_235 6 SER C 33 0.5 12.011 ; > qtot 0.5 > 90 opls_238 7 NAC N 34 -0.5 14.0067 ; > qtot -0.5 > 92 opls_242 7 NAC CH3 35 0.02 12.011 ; > qtot -0.18 > In rtp file all the atomtypes are there in corresponding residues however in > ffoplsaabon.itp, I could not find an entry in dihedral types for these > dihedrals. > > Regards, > Gurpreet Singh > > > > > > > > > Check your topology file against ffoplsaa.rtp and ffoplsaabon.itp > > Yang Ye > > singh wrote: > > > > Dear Users, > > > > I am trying to simulate a capped pentapeptide using OPLS force field. > > Pdb2gmx runs successfully , however grompp gives following warnings > > > > WARNING 1 [file "topol.top", line 632]: > > > > No default Ryckaert-Bell. types, using zeroes > > > > WARNING 2 [file "topol.top", line 857]: > > > > No default Ryckaert-Bell. types, using zeroes > > > > > > > > How should I proceed if these parameters are missing in OPLS. > > > > The topology and gro files are attached herewith > > > > > > > > Regards, > > > > Gurpreet > > > > ------------------------------------------------- > > > > University of Dortmund > > Department of Chemistry > > Physical Chemistry I - Biophysical Chemistry > > Otto-Hahn Str. 6 > > D-44227 Dortmund > > Germany > > > > Office: C1-06 room 176 > > Phone: +49 231 755 3916 > > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
