Thank you Justin. At the mean time I had another error after grompp, "ERROR 1 [file topol_Protein_chain_E.itp, line 52165]: Unknown cmap torsion between atoms 3022 3024 3026 3046 3049"
the 3022 3024 3026 3046 3049 in the itp files referred to the backbone (C-N-CA-C-N) of three connected residues R-W-T.. I looked at the backbone of the pdb and it looks alright. this error didn't show up until today when i work from home using gromacs on another server. DO you think if this is caused by different versions? On Sun, Nov 26, 2017 at 9:38 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/26/17 9:32 AM, MD wrote: > >> Thank you Mark. >> >> Do you think if the atom types of HE, OE and SG are correct in my >> merged.rtp? These are the three atoms which have name changing cause of >> the >> inserted sulfur. I modified their atom types as well. I need to make sure >> the type names are correct before I add the bond types in ffbonded.itp. >> > > O is the carbonyl oxygen type in CHARMM, so I doubt that's a wise choice. > You may also need an entirely different sulfur atom type. Have you assessed > QM water interactions and dipole moments? Where did these charges come > from? If you haven't done so already, you need to do some really basic > validation before attempting to do anything with bonded parameters. The > dihedrals will be particularly sensitive to the quality of LJ and charge > terms. > > -Justin > > > [ 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 >> SG CB >> SG OE >> N HN >> N CA >> C CA >> C +N >> CA HA >> CB HB1 >> CB HB2 >> OE HE1 >> O C >> >> >> On Thu, Nov 23, 2017 at 12:25 AM, Mark Abraham <mark.j.abra...@gmail.com> >> wrote: >> >> Hi, >>> >>> You need to specify each bond you want, and for the types of those bonds >>> to >>> have parameters available. Bonds are specified with atoms, bond types are >>> specified with atom types. >>> >>> Mark >>> >>> On Thu, 23 Nov 2017 04:22 MD <refm...@gmail.com> wrote: >>> >>> Yes. You are right about the names. I wrote them by memory and they were >>>> not printed from the terminal. I will try to edit the ffbonded.itp and >>>> >>> see >>> >>>> how it goes. Thanks! >>>> Ming >>>> >>>> On Wed, Nov 22, 2017 at 10:14 PM, Justin Lemkul <jalem...@vt.edu> >>>> wrote: >>>> >>>> >>>>> On 11/22/17 10:11 PM, MD wrote: >>>>> >>>>> 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 >>>>>> >>>>>> Make sure you're clear on what needs to be done, because what you've >>>>> written above is not correct and would never be printed - your dihedral >>>>> >>>> is >>>> >>>>> a mix of types and names. All parameters are assigned by type, never by >>>>> name. >>>>> >>>>> 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? >>>>>> >>>>>> ffbonded.itp >>>>> >>>>> >>>>> -Justin >>>>> >>>>> 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. >>>>>>> >>>>>>> >>>>>>> -- >>>>> ================================================== >>>>> >>>>> 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. >>>> >>> -- >>> 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? 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