[gmx-users] Re: One molculetype for 3 proteins

Steven Neumann s.neumann08 at gmail.com
Thu May 24 17:32:36 CEST 2012

On Thu, May 24, 2012 at 3:42 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Dear Gmx Users,
> I want to use distance restraints of 3 atoms which belong to 3 different
> proteins. For this purpose I want to create one topology so one
> moleculetype:
> I tried to use pdb2gmx -chainsep ter (where i put TER after each chain in
> my PDB)
> But 3 separate topologies were created.
> I want to adjust proper charges for each teraminals but pdb2gmx without
> -chainsep will treat it as a one molecule.
> Please help.
> Steven
It is stated:

The separation of chains is not entirely trivial since the markup in
user-generated PDB files frequently varies and sometimes it is desirable to
merge entries across a TER record, for instance if you want a disulfide
bridge or *distance restraints* between two protein chains or if you have a
HEME group bound to a protein. In such cases multiple chains should be
contained in a single molecule_type definition. To handle this, pdb2gmx has
an option -chainsep so you can choose whether a new chain should start when
we find a TER record, when the chain id changes, combinations of either or
both of these or fully interactively.

And if I use:

pdb2gmx -chainsep

In my topology:

; Include chain topologies
#include "topol_Protein.itp"
#include "topol_Protein2.itp"
#include "topol_Protein3.itp"

[ molecules ]
; Compound        #mols
Protein             1
Protein2            1
Protein3            1

So how can I have one [moleculetype] for the usage of distance restraints?
Why do they state that this option will allow to have one [moleculetype] ?

Please, help

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