[gmx-users] QM/MM error: no such bonded interactions with 5 atoms (Mark Abraham)

[Groenhof, Gerrit]

Hi,

The problem is that the QM/MM code checks all bonded interactions until 4 atoms, which at the time it was implemented, was the maximum, i.e. before CMAP.

However, I am not sure whether  the CMAP interactions should be in or excluded. Excluding will alter the backbone energetics in your QM/Charmm calculations, while including could lead to spurious interactions.

In both cases, in gmxpreprocess/topio.c one needs to  add a case 5 to the switch(nratoms) in the generate_qmexcl_moltype in which one either keeps this interaction, or removes it.

best,

Gerrit

Hi,

CHARMM27 uses CMAP dihedrals that have 5 atoms. How that relates to your
topology isn't clear on the information you've provided. In what context
did you get the error message?

Mark

On Thu, Mar 10, 2016 at 12:58 PM Roman Zeiss <romanzeiss at gmx.net> wrote:

> Dear Gromacs users,
>
> I am trying to set up a QM/MM simulation on Gromacs 5.0.4 with Charmm27. I
> get the error "no such bonded interactions with 5 atoms" when I try to run
> the simulation. What I did so far:
>
> 1. I modified the force field files atomtypes.atp and ffnonbonded.itp to
> include the atom type "LA" and also added a residue file "la.rtp".
>
> 2. In my topology file for the Protein I have (after adding the LA atoms
> to that chain at position 1763 and 1764):
> [ virtual_sites2 ]
> ; LA QMatom MMatom func length
> 1763    30  32  1   0.65
> 1764    1747    1745    1   0.65
> [ constraints ]
> ; QMatom MMatom func length
> 30  32  2   0.153
> 1747    1745    2   0.153
>
> 3. Then I created an index.ndx with a group [ QMatoms ].
>
> 4. For all bonds between QMatoms I changed the bond type from 1 to 5.
>
> Do I have to change anything more like dihedrals or something? Maybe
> delete bonds/dihedrals containing the connecting atoms? But nothing so far
> changed the error message.
>
> I appreciate any kind of advice very much!
> Thanky you and best regards,
> Roman
>
>
>
>
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End of gromacs.org_gmx-users Digest, Vol 143, Issue 43
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