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? 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