Justin, originally I did use SG and OE in the [bonds] and I got complaints of "SG-OE no default bond type" "CB SG OE" no default U-B type and "CT1, CT2, SG, OE" no default proper dihedral gypes. Are these the parameters you mean that are missing? If so, what files do you think I should modify to create these parameters? ffbonded.itp, merged.rtp and residuetype.dat?
On Wed, Nov 22, 2017 at 10:01 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/22/17 9:57 PM, MD wrote: > >> Thanks Justin. Then do I need to create new bond of SG and OE in >> ffbonded.itp? Cause I have tried adding SG and OE bond in ffbonded.itp >> and >> > > SG and OE are atom names, not types. That's not a valid approach. > > I got complaint from gromacs.. I modified the SG-OE bond from S-O bond and >> it should work... >> > > The [bonds] section requires atom names in order to function, so use of SG > and OE here is correct (your original entry used S and O, which are atom > types and therefore not correct). If grompp subsequently complains about > missing force field parameters when the correct bonds are written to the > topology, then what you're attempting to do is not supported by the force > field and you will have to either parametrize those missing interactions or > find parameters. > > -Justin > > > On Wed, Nov 22, 2017 at 9:42 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 11/22/17 9:32 PM, MD wrote: >>> >>> Hi gromacs folks, >>>> >>>> I was trying to introduce sulfenic acid as modified cysteine to the >>>> forcefield as following. Everything went well until the "gmx mdrun -v >>>> -deffnm em". The only file I modified was merged.rtp since there were no >>>> new bond or dihedral angles. However my sulfenic acid falls apart >>>> (oxygen >>>> and sulfur are far away from the protein) after mdrun. Any help or >>>> suggestions what I should do next? I am reading the manual at the same >>>> time >>>> but I thought maybe I can get some help here as well. >>>> >>>> Thank you for your time and any advice will be appreciated. >>>> >>>> Ming >>>> >>>> [ CSO ] >>>> [ atoms ] >>>> N NH1 -0.470 0 >>>> HN H 0.310 1 >>>> CA CT1 0.070 2 >>>> HA HB1 0.090 3 >>>> CB CT2 -0.110 4 >>>> HB1 HA2 0.090 5 >>>> HB2 HA2 0.090 6 >>>> SG S 0.6 7 >>>> OE O -0.83 8 >>>> HE1 H 0.160 9 >>>> C C 0.510 10 >>>> O O -0.510 11 >>>> [ bonds ] >>>> CB CA >>>> S CB >>>> S O >>>> N HN >>>> N CA >>>> C CA >>>> C +N >>>> CA HA >>>> CB HB1 >>>> CB HB2 >>>> OE HE1 >>>> O C >>>> >>>> You need a bond between SG and OE. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> ================================================== >>> >>> -- >>> 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. >>> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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.