Is there any way to remove all the hydrogen atoms present in a pdb file using VMD or ovito.
You can delete atoms in modeling software like Vesta, materials studio, etc.
In Ovito,
add modification --> "select type" under selection and select the atom type you want to remove -- they will be highlighted
and then add --> delete selected under modification -- atoms will be deleted
after that export file as ".xyz" or "Lammps data file" as per your requirement.
Thanks Nitin Luhadiya . But the associated bonds, angles, and dihedrals are also needed to be deleted. Can it do that?
As far as I know, you need to obtain the professional version if you want to hide some arbitrary bonds in the OVITO app.
Anyway, you can hide the same-type bonds by reducing the size of bonds up to zero, and that is the easiest way to hide objects in OVITO,
VMD has a psfgen utility that can do what you want but all of the bonds, angles and dihedrals are defined by the residues within the topology files. What you are asking to do is chemically inconsistent: -CH2-OH => =C=O , for example. These two fragments will not behave in the same fashion dynamically. So, what is your objective? Are you thinking to produce some sort of coarse-grained model with new atom types? OH and CH2, for example? In that case, go read about coarse-grained simulations, for which there are many examples.
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