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

banijamali_fs banijamali_fs at ut.ac.ir
Mon Dec 10 19:04:57 CET 2018

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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