[gmx-users] Unknown bond_atomtype

Nash, Anthony a.nash at ucl.ac.uk
Wed Feb 17 23:12:00 CET 2016 

Hi,

Thanks for the information, Mark. I fully parameterised the bonded terms
using QM data and some software I wrote. Now that I’ve sorted out
ffnonbonded [atomtypes], all that remains are some missing angle terms. I
want to have the forcefield files correct so an MD simulation can be
generated with very little changes to the topol file after running
pdb2gmx. I do have a couple of questions that I hope you could help me
with. 

1) For grompp to compile successfully, must every molecule/residue have a
complete set of dihedral angle force constants?
2) It appears as though the residue to residue bond connectivity in my
force field files aren’t correctly parameterised. In NGLY-MOD-CGLY, a
bonded term is added to the topol for the C in NGLY to the N in CGLY. To
avoid this must I add an entry such as -C N in the [ bonds ] section of
the [ MOD1 ] residue definition in aminoacids.rtp? I’m unsure what “-C”
means.

Thanks for all your help.

Anthony


Dr Anthony Nash
Department of Chemistry
University College London





On 17/02/2016 21:46, "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,
>
>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
>> >>>>
>> >>>>
>> >>>>
>> >>>> --
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