[gmx-users] Editing of the existing system

James Starlight jmsstarlight at gmail.com
Fri Mar 30 16:00:53 CEST 2012


Also I'd like to know some more about most correct parametrisation of such
new edited system. My new system consist of two proteins ( one- wich was
initially and the second small peptide wich I've docked to the first
protein). So now I need to define 2 separate groups for the below enties of
my MD files

energygrps = Protein peptide

tc-grps     = Protein_Bilayer SOL_ions_peptide

and finally CoM groups because of the general anisotropy of the membrane system

comm-grps	= Protein_Bilayer SOL_Ions_Peptide

I've made itp file for the peptide via pdb2gmx so in th default
definition both the protein and peptide are the protein enty in the
index file.

I've separate both of the protein and peptide by selection of two
subsets of atoms wich represent to the each of that enties.

So finally I have two groups in the index.ndx file

a_1-5000  ( it's protein)
a_9999-10500 (it's peptide)

Does this separation correct in general ? I have some fears because
both protein and peptide consist of the same residue numbers in the
GRO file ( e.g there are 212- lys wich is part of the protein and
212-Pro wich is part of the peptide ) Might this system be tended to
I have no errors during processing of that sustem by grompp as well as
md run. What should I do for such system consisted of two proteins in
separate phases ( membrane-like and water)

Thanks for help again,


30 марта 2012 г. 17:34 пользователь Mark Abraham
<Mark.Abraham at anu.edu.au>написал:

> Constructing a system is normally easiest if you remove all your
> solvent(s), paste in your interesting molecules somehow or other, and then
> rebuild the solvent with tools like genbox.
> Mark
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