[gmx-users] Re: One molculetype for 3 proteins
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
> 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.
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:
In my topology:
; Include chain topologies
[ molecules ]
; Compound #mols
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] ?
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