[gmx-users] problem with introducing a new structure in gromacs, please help if anybody knows

Dallas Warren dallas.warren at monash.edu
Tue Dec 11 00:04:05 CET 2018

The overall charge for an entire molecule has to be an integer value,
anything other than that is physically impossible.  So you have to fix your
charges so that is the case, and you must have done something wrong where
you pull/calculated the charges.

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 Tue, 11 Dec 2018 at 05:05, banijamali_fs <banijamali_fs at ut.ac.ir> wrote:

> Hi there,
> I'm working on MOFs ( metal organic frameworks) with gromacs, before
> starting the simulation, I should introduce my molecule in
> aminoacids.rtp file, that I did it, my problem is I have 4 repetitive
> structures (Ligands) and 2 metals, the whole charge of molecule is zero
> but every one of ligands has -1 charge and the two metals, every one of
> them has +2 charge, with this explanation, when I want to define one of
> repetitive ligands in aminoacids.rtp file, it should be -1 to get proper
> results, but from DFT calculations, when I put the partial charges of
> every one of atoms, the sum is not -1, at the end I want to know that,
> first, is it problem? I mean in the other steps of simulation, I get
> error? or it's not a problem, or if anybody knows that what should I do,
> please guide me with this problem.
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