[gmx-users] Charges and Antechamber
joao.m.a.henriques at gmail.com
Tue Oct 3 17:41:32 CEST 2017
Or this... :) I've never used it, but I'm sure it works like a charm. I
personally prefer to be more involved in all stages of the process, but I'm
a bit old school and I like to avoid "black boxes" for my own learning
benefit. That being said, I'm sure it does the job and it's faster &
simpler. It's probably the best way to go for someone with less experience
with this sort of task.
On Oct 3, 2017 5:10 PM, "ABEL Stephane" <Stephane.ABEL at cea.fr> wrote:
It is quite easy to derive RESP charges and use them with GROMACS. You
could follow the steps
1) Build a pdb file of your molecule/modified residue
2) Use the web server pyRED (http://upjv.q4md-
forcefieldtools.org/REDServer-Development/) and derive the RESP charges.
The webserver will also give you all the necessary parameters of the ff
(mol2 file, atom types, (non)bonded parameters)
3) Use these parameters to construct a rtp file for GROMACS for a given
4) and finally use pdb2gmx with the pdb file to obtain the itp file.
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