[gmx-users] Load GROMACS trajectory with atom types and water in VMD
m.ebert at umontreal.ca
Thu Sep 24 22:56:09 CEST 2015
for the implicit ligand sampling module in VMD you need a loaded trajectory with the correct atom types. i guess I have to load them manually from another file into VMD.
> On Sep 24, 2015, at 4:43 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> You can get what is in the structure file, and that is all. Since the atom
> name is not the name of the force-field atom type, I don't think you can do
> what you want. It is likely that whatever you were planning to do with atom
> types you can do with the VMD selection syntax.
> On Thu, Sep 24, 2015 at 10:28 PM Ebert Maximilian <m.ebert at umontreal.ca>
>> Dear list,
>> I am not sure if this is a question for the VMD or GROMACS mailing list.
>> However, I try to load a trr/xtc trajectory into VMD and want to keep the
>> atom types. Since top and tpr files are not an input for VMD the atom type
>> and name is the same as the structure file is PDB or GRO. I also tried
>> top2psf but I guess since I have water and need the water in the trajectory
>> I can’t use the script. Any idea how I could load the atom types?
>> Thank you very much.
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