[gmx-users] qm/mm LA not found (Sylwia Kacprzak)

Groenhof, Gerrit ggroenh at gwdg.de
Mon Nov 7 15:53:35 CET 2016


Do I understand correctly that the grompp complains about a bond that is still bond type 1?

If so, then the error message suggests that grompp cannot access a ff*bin.itp with the parameters for the atom pair.

Usually you'd also get additional errors for missing angle and torsion types. Do you get those?

Can you run without QM/MM, i.e. a 'normal' MM simulations with this topology?


Hi Gerrit,

thank you for your hint. There was no LA entry in the ff*nb.it file. I
have added it there.
But now I get a new error. I have a protein with cofactor. Part of the
cofactor is in QM part
and the rest in MM. For the cofactor I have a separate *itp file as for
the rest of protein.
By preparing the calculation I get and error for all MM atoms:

ERROR 1 [file DRGGMX_groups_v3_QMMM.itp, line 133]:
   No default Bond types

example from *itp file

[ bonds ]
; ai  aj  fu    c0, c1, ...
   21  22   5     ;   C9A  N10
   22  23   5     ;   N10  C1' ;'
   24  23   1     ;   C2'  C1'
   24  25   1     ;   C2'  O2'

There is no error for atoms with bond type 5, but for all with bond type 1.


On 11/05/2016 03:40 PM, Groenhof, Gerrit wrote:
> Is the LA also defined for the force field you're using? Can you check whether there is a LA entry in the ff*nb.it of the force field? If not, add it there manually.
> Best,
> gerrit
> Message: 2
> Date: Fri, 4 Nov 2016 16:10:03 +0100
> From: Sylwia Kacprzak <sylwia.kacprzak at physchem.uni-freiburg.de>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] qm/mm LA not found
> Message-ID: <581CA4CB.2050002 at physchem.uni-freiburg.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
> Dear all,
> I have set qm/mm calculations with Gromacs 5.1.4 and Orca.
> I treat first the full cofactor on a QM level. However when I cut the
> bond to take only part of it for QM and
> introduce link atom according to the manual with link atom (LA) I get
> following error.
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1.4
> Source code file:
> /home/widu/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line: 1345
> Fatal error:
> Atomtype LA not found
> Any ideas?
> Greetings
> Sylwia


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