[gmx-users] using more than one type of molecules
amberquestion at yahoo.com
Fri Mar 13 19:14:20 CET 2009
new to Gromacs and have some questions to learn the answers. I study
on one type molecule. If I want to add lets say 240 molecules, which
is the best way to use editconf or genbox ? And I learned the
procedure of using more than one type of molecules in gromacs. But
I'm not sure, so I'm waiting for your contributions. Assume that I
have two small organic molecules like hydrocarbons X and Y. I think
First I will have to get seperately DRGGMX.ITP and DRGPOH.PDB for
the each molecules in different work directories. Then chose one
directory ( X ) and do the operations like in ''GROMACS Tutorial for
Drug – Enzyme Complex'' Then in this command
–cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top
I get gmx.pdb gmx.top files I will add #include “Y.itp” and
editing the number of Y molecule and go on ..
you please help me to learn the true process of using more than one
type of molecules in gromacs ?
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