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

[Sylwia Kacprzak]

Hi Gerrit,

yes, grompp complains only about bond type 1. It gives only error for
lines where the bond types are described, nothing about angle or torsion 
types.
I was able to run normal MM, as well as QM/MM if I get the whole 
cofactor in QM
region, meaning if all bond types in cofactor are type 5 it runs without 
problems.

Greetings
Sylwia


On 07.11.2016 14:50, Groenhof, Gerrit wrote:
> Hi,
>
> 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?
>
> Gerrit
>
>
> 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.
>
> Greetings
> Sylwia
>
>
> 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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