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

[Tsjerk Wassenaar]

Hi Steven,

So it did what you told it to do. You want -chainsep no or none. Doing
it from the top of my head, so I'm not sure. But it'll be listed in
the help what options there are.

Cheers,

Tsjerk

On Thu, May 24, 2012 at 8:29 PM, Steven Neumann <s.neumann08 at gmail.com> wrote:
>
>
> 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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>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands