[gmx-users] Unknown bond_atomtype

Mark Abraham mark.j.abraham at gmail.com
Wed Feb 17 22:46:22 CET 2016 

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.nash at 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-bounces at maillist.sys.kth.se on
> behalf of Nash, Anthony"
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> a.nash at 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-bounces at maillist.sys.kth.se
> on
> >behalf of Nash, Anthony"
> ><gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> >a.nash at 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-bounces at maillist.sys.kth.se
> >>on
> >>behalf of Mark Abraham"
> >><gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> >>on behalf of mark.j.abraham at 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.nash at 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-request at 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-request at 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-request at 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-request at 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list