[gmx-users] qm/mm LA not found (Sylwia Kacprzak)
Sylwia.Kacprzak at physchem.uni-freiburg.de
Mon Nov 7 18:44:34 CET 2016
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
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
On 07.11.2016 14:50, Groenhof, Gerrit wrote:
> 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.
>> 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?
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> End of gromacs.org_gmx-users Digest, Vol 151, Issue 22
More information about the gromacs.org_gmx-users