Hi, Your MOD residues are LYS connected by a ring, so the atom types and bonds sections should be pretty much as for LYS, with the ring parts perhaps along the lines of TYR. If you have done a full parameterization somehow and have specialized atom types, then yes, those bonded and non-bonded parameters need to go into the databases for grompp to look up (or then can also go in the [bonds] section of the .rtp, I think).
Mark On Wed, Feb 17, 2016 at 10:39 PM Nash, Anthony <a.n...@ucl.ac.uk> wrote: > > Dear Mark, > > > I didn’t expect the problem was in ffnonbonded.itp. Problem solved. Thanks > for the earlier hint. > > Anthony > > On 17/02/2016 18:01, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on > behalf of Nash, Anthony" > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > a.n...@ucl.ac.uk> wrote: > > >Hi Mark, > > > >Further to my earlier email. I’ve answered the query as to whether atom > >types and names can be the same. This is fine, judging by The N N and O O > >in all of the amino acid types. > > > >I suspect I either have an additional problem or I have identified the > >root cause of my original problem. Every non-terminal amino acid has a -C > >N line in [ bonds ]. My custom residue does not. I assume this is to do > >with amino acid connectivity. How do I implement this single bond if I > >have the connectivity NGLY-MOD-CGLY, where EVERY atom in MOD is completely > >new? I assume this is where you meant use existing types. So in theory I > >could just change the very first atom of MOD, which would be MN1 to N, and > >then go into ffbonded and just change MN1-MC1 to N-MC1 for the first bond > >parameter the MOD residue. > > > >Apologies for rambling on, I *think* I know what I am doing. > > > >Thanks > >Anthony > > > >Dr Anthony Nash > >Department of Chemistry > >University College London > > > > > > > > > > > >On 17/02/2016 17:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on > >behalf of Nash, Anthony" > ><gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > >a.n...@ucl.ac.uk> wrote: > > > >>Hi Mark, > >> > >>Thanks for the reply. I’m a little confused when you say “Choose existing > >>types”. Are you saying that I am confined to only those atom types that > >>come along with the forcefield upon installation, or that I can add new > >>types but I’ve made a slight mishap between when specifying them within > >>the [atom] section of my new residue? > >> > >>Also, I am guessing there is no issue with atom NAME and TYPE being > >>identical? > >> > >>Many thanks > >>Anthony > >> > >>Dr Anthony Nash > >>Department of Chemistry > >>University College London > >> > >> > >> > >> > >> > >>On 17/02/2016 16:43, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se > >>on > >>behalf of Mark Abraham" > >><gromacs.org_gmx-users-boun...@maillist.sys.kth.se > >>on behalf of mark.j.abra...@gmail.com> wrote: > >> > >>>Hi, > >>> > >>>You've specified a type for your atom in [atoms] and elsewhere a bond > >>>that > >>>uses it. Grompp has to find parameters for a bond between those two > >>>types, > >>>etc. Choose existing types ;-) > >>> > >>>Mark > >>> > >>>On Wed, 17 Feb 2016 17:27 Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >>> > >>>> Hi all, > >>>> > >>>> As per a previous email (cross linking two peptide chains), I¹ve > >>>>created a > >>>> brand new crosslink (think disulphide bond) residue from scratch. I > >>>>have > >>>> defined it in all the files necessary (.rtp, residuetypes, specbond, > >>>> atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no > >>>> problems. > >>>> > >>>> Unfortunately when I run grompp (5.0.4) I get the following error: > >>>> > >>>> Fatal error: > >>>> Unknown bond_atomtype MN1 <‹‹ first atom in my new residue > >>>> > >>>> > >>>> At first I thought my topology might be pointing to the wrong > >>>>forcefield, > >>>> but I¹ve checked and double checked: > >>>> > >>>> #include > >>>>"/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp" > >>>> #include "modic.itp" > >>>> ;#ifdef POSRES > >>>> ;#include "posre.itp" > >>>> ;#endif > >>>> > >>>> [ system ] > >>>> ; Name > >>>> MODIC with glycine terminal ends > >>>> > >>>> [ molecules ] > >>>> ; Compound #mols > >>>> MODIC 1 > >>>> > >>>> > >>>> I¹m going to take a guess at what the problem is. Each of the atoms in > >>>>the > >>>> residue was derived from scratch.Therefore, they have a completely new > >>>> type. I wasn¹t feeling very creative with my naming convention so the > >>>>atom > >>>> name and the atom type are identical e.g., > >>>> > >>>> ;MODIC crosslink > >>>> [ MOD1 ] > >>>> [ atoms ] > >>>> ; NAME TYPE CHARGE NUMBER > >>>> MN1 MN1 -0.3640 1 > >>>> MC1 MC1 0.0358 2 > >>>> MC15 MC15 0.4871 3 > >>>> Š > >>>> > >>>> Š > >>>> > >>>> Will this have confused grompp? > >>>> > >>>> Many thanks > >>>> Anthony > >>>> > >>>> Dr Anthony Nash > >>>> Department of Chemistry > >>>> University College London > >>>> > >>>> > >>>> > >>>> -- > >>>> 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. > > > >-- > >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.
