[gmx-users] Regarding multiple ligands' topology

Justin Lemkul jalemkul at vt.edu
Fri Nov 8 12:21:44 CET 2019



On 11/8/19 2:38 AM, Mijiddorj B wrote:
> Dear GMX users,
>
> I would like to use multiple small molecules in the simulation system. The
> topology files of the ligands were generated by swissparam. However, grompp
> could not recognize the second ligand topology during the preparation of
> system and gives following message:
> ########
> '[ atomtypes ]'
> Invalid order for directive atomtypes
> ########
>
> How can overcome this problem?

http://manual.gromacs.org/current/user-guide/run-time-errors.html#invalid-order-for-directive-xxx

Combine all of the new atom types in one file that is #included in the 
correct order.

-Justin

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Justin A. Lemkul, Ph.D.
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