[gmx-users] Error in energy minimization step/could anyone help me

[Dallas Warren]

The molecule name you have in  your .top file, in the [ molecules ]
section, does not match the molecule name in your .itp (could also be
within your .top) file, in the [ moleculetype ] section.

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 Mon, 25 Feb 2019 at 02:24, banijamali_fs <banijamali_fs at ut.ac.ir> wrote:

> Hi there,
>
> I'm simulating the adsorption of H2 on a structure (Metal organic frame
> work), after making the pdb structure and running the first cmmand of
> gromacs to have gro file, I added two atoms of CU and one hydrogen
> molecule to the gro file and also changed the number of the atoms at the
> top of gro file. Then I run the following commands up to the command
> about energy minimization that I got this error( No such molecule type
> hydrogen), I want to ask that, gromacs knows H2 molecule, why it says
> that, no such molecule type? it means that I should introduce it agin in
> aminoacids.rtp file?
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