[gmx-users] Unknown bond_atomtype

[Nash, Anthony]

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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