[gmx-users] Minimization Problem

[Dallas Warren]

Where did you obtain the topology from? What forcefield is it meant to
be used with?  Does that forcefield include bonds between those atom
types?

The error is occurring because when grompp goes through the topology,
it cannot match up the atom types that are bonded together, with an
existing bond within the forcefield.

Easiest solution is to get a topology for that molecule, for the
forcefield you want to use, that someone else has built. Or you could
specify that bonds yourself within the topology.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 10 October 2017 at 04:55, Ednilsom Orestes <eorestes at gmail.com> wrote:
> Dear Gromacs community
>
> I am trying to run a simulation of choline molecule but found various
> errors concerning to bonds, angles and dihedrals during the minimization.
>
>
>
> Part of the top file (line number in the first column):
> ...
> 29 [ bonds ]
> 30;  ai    aj funct
> 31    1      4     1    ;     N   CT3
> 32    1    14     1    ;     N   CT4
> 33    1      2     1    ;     N   CT1
> 34    1      3     1    ;     N   CT2
> 35    2    12     1    ;   CT1  HC12
> 36    2    13     1    ;   CT1  HC11
> 37    2    11     1    ;   CT1  HC13
> 38    3      7     1    ;   CT2  HC21
> 39    3      6     1    ;   CT2  HC22
> 40    3      5     1    ;   CT2  HC23
> 41    4      8     1    ;   CT3  HC31
> 42    4    10     1    ;   CT3  HC32
> 43    4      9     1    ;   CT3  HC33
> 44   14    17     1    ;   CT4  HC41
> 45   14    15     1    ;   CT4   CT5
> 46   14    16     1    ;   CT4  HC42
> 47   15    20     1    ;   CT5  HC51
> 48   15    18     1    ;   CT5    OH
> 49   15    19     1    ;   CT5  HC52
> 50   21    18     1    ;    HO    OH
> ...
>
>
> Errors:
>
> ERROR 1 [file topol_choline.top, line 49]:
>     No Default Bond type
>
> ERROR 2 [file topol_choline.top, line50]:
>     No Default Bond type
>
> and so on with some of the angles and dihedrals...
>
> Does anybody have a clue on how to fix it?
>
> Thanks in advance.
>
> Ednilsom
> --
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