[gmx-users] Unknown bond_atomtype

[Nash, Anthony]

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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