[gmx-users] Regarding .itp file to the system

Mark Abraham mark.j.abraham at gmail.com
Mon Dec 14 12:39:51 CET 2015


You need to end up with a file that has the coordinates of the protein, and
then the coordinates of the ligand, to match the order of your [system]
directive in the topology file. How best to do that depends how you plan to
choose your starting configuration.


On Mon, Dec 14, 2015 at 10:22 PM Alex Mathew <alexmathewmd at gmail.com> wrote:

> Dear Justin,
> Thanks for  your previous answer i quoted below
> "1. Process the protein with pdb2gmx and obtain a .top and coordinate file
> in
> whatever format you like.
> 2. Generate a ligand topology, #include its .itp file in the .top
> 3. Append the ligand coordinates to those of the protein from step (1);
> again
> format is irrelevant"
> i have done first two steps ,i done with pdb2gmx for the protein
> added .itp file to topol.top as
> *; Include ligand topology
> #include "molecule.itp"*
> i don't understand the third step ,could you please elaborate little
> more,sorry i couldn't understand it.
> Thanks
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