Thank you for the clarification. There’s a good chance there is more to this scenario but I recall making polymers ( with Avogagdo ) , using pdb2gmx to create the top ( then itp ) and sometimes having the same error as the OP mentioned. The errors were eliminated by adding the unfound type with atomname2type.n2t
I should be able to post the sequence of events if you think it useful to others. Paul > On Dec 15, 2019, at 11:39 AM, Justin Lemkul <[email protected]> wrote: > > > > On 12/14/19 1:14 PM, Paul Buscemi wrote: >> If the itp is correct then modify atomnames2types to add the correct bonds >> and bond lengths > > The atomname2type.n2t file is only relevant with x2top, but the OP already > has a topology, so this is not the issue. If you mean the .atp file, then > this too is not relevant because pdb2gmx is the only program that reads this. > > -Justin > >> PB >> >>> On Dec 13, 2019, at 7:52 PM, Justin Lemkul <[email protected]> wrote: >>> >>> >>> >>>> On 12/13/19 2:18 AM, Muthusankar wrote: >>>> Dear Gromacs users, >>>> I am simulating a protein-ligand complex and performing the grompp command >>>> before adding ions to the system. I got the error. >>>> *Fatal error: *(file: ligand.itp) >>>> Atomtype *CH2 not found*. >>>> *command used:* >>>> gmx grompp -f ions.mdp -c protein_box.gro -p protein.top -o ions.tpr >>>> >>>> Please guide me, How to rectify the problem. >>>> >>> This means you're trying to use an atom type that your force field doesn't >>> recognize. Either you're mixing and matching force fields (never do this) >>> or your ligand topology relies on new atom types that should be introduced >>> into the force field, in which case the source of the ligand topology >>> (server, etc.) should provide that information. >>> >>> -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 >>> >>> [email protected] | (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 [email protected]. > > -- > ================================================== > > 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 > > [email protected] | (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 [email protected]. -- 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 [email protected].
