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

Dallas Warren dallas.warren at monash.edu
Sun Feb 24 22:35:02 CET 2019

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

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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