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

[Steven Neumann]

On Thu, May 24, 2012 at 6:05 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Steven,
>
> Doesn't -chainsep take an argument?
>
> Cheers,
>
> Tsjerk
>

It does, I used option: -chainsep ter
And I had in my pdb file after each chain TER and thus 3 itp files were
created corresponding to my top file and representing different
moleculetype (protein, protein2, protein3). In order to use distance
restraints I want to have one moleculetype with 3 chains which are not
connected via bonds and adjust proper charges to each of 6 terminals. Any
suggestions?

Steven

> On May 24, 2012 5:33 PM, "Steven Neumann" <s.neumann08 at gmail.com> wrote:
>
> On Thu, May 24, 2012 at 3:42 PM, Steven Neumann <s.neumann08 at gmail.com>
> wrote: > > Dear Gmx Users,...
> 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
>
> Steven
>
>
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