I want to perform implicit simulation for a protein-ligand complex.
for a protein alone, implicit works fine, but for ligand atoms it shows error as copied below,
Setting gen_seed to -1914387900
Velocities were taken from a Maxwell distribution at 300 K
GB parameter(s) missing or negative for atom type 'N3'
GB parameter(s) missing or negative for atom type 'H'
GB parameter(s) missing or negative for atom type 'CT'
GB parameter(s) missing or negative for atom type 'HP'
GB parameter(s) missing or negative for atom type 'HC'
GB parameter(s) missing or negative for atom type 'H1'
GB parameter(s) missing or negative for atom type 'S'
GB parameter(s) missing or negative for atom type 'C'
GB parameter(s) missing or negative for atom type 'O'
GB parameter(s) missing or negative for atom type 'OH'
GB parameter(s) missing or negative for atom type 'HO'
GB parameter(s) missing or negative for atom type 'H5'
GB parameter(s) missing or negative for atom type 'H4'
GB parameter(s) missing or negative for atom type 'HA'
GB parameter(s) missing or negative for atom type 'MG'
GB parameter(s) missing or negative for atom type 'P'
GB parameter(s) missing or negative for atom type 'OS'
GB parameter(s) missing or negative for atom type 'H2'
GB parameter(s) missing or negative for atom type 'c1'
Program: gmx grompp, version 2016.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1296)
Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 19 atomtypes or they might be negative.
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I would just like to add that the use of metal ions in implicit solvent simulations is in general a Bad Idea. Their parameterisation is simply not up to the task - without a layer of solvating water molecules, their interactions with protein atoms become far, far too strong. I've experimented quite a few times with magnesium ions in interactive implicit solvent simulations in the context of fitting electron density maps. Even when the density map is at very high resolution and pulling very strongly on the atoms, a magnesium ion placed in a clear density peak will be ripped out of position to stick to acidic sidechain atoms 3 Angstroms or more away - or conversely, if the magnesium is fixed in space the acidic sidechains will be pulled towards it, hopelessly distorting the structure in the process. The interaction with species like ATP is even worse - in an implicit solvent environment the excessive electrostatic attraction will twist a Mg-ATP complex up into a completely unphysical pretzel.
I would advise to carefully rethink your experiment.
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