[gmx-users] Unknown bond_atomtype

[Nash, Anthony]

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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