[gmx-users] monomer's conectivity

[Justin A. Lemkul]

Andrea Muntean wrote:
> Thank you. I hope this helps me further.
> My system is 32 polystyrene chains of 80 monomers.

Mark's suggestion about generating an .rtp entry is a good one for your 
purposes, then.  Also search the list archive for "polymer" or "polystyrene" and 
you will find many pertinent discussions involving people who have done what you 
need to do, and the problems they faced along the way.

-Justin

> Andrea
> 2008/10/23 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
> 
>     Andrea Muntean wrote:
> 
>         Thank you for your answer.
>          If I am looking at the PDB standard format and my file, I
>         observe that I have only one number between the type of residue
>         and coordinates, and I suppose it is the residue current number.
>         I am indeed missing the chain identifier code, which should be
>         of A1 Fortran format, which I don't really understand (one
>         carachter, but I have 32 chains, so it should be minimum A2 or
>         I2). That I could introduce.
> 
> 
>     Get a PDB file with just one polymer molecule and work on getting a
>     topology for that. Walking before running :-)
> 
> 
>         In my pdb entries I dont define any connectors. Should they be a
>         dummy atom, with the corresponding bond, angle, dihedhral, which
>         after that I redefine in the tdb file?
> 
> 
>     First you need a functional *residue topology*. Check chapter 5 of
>     the manual and look at the other force fields to see how (for
>     example) protein force fields define the connectors with + and -
>     prefixes. Once you've got that, then it's possible for pdb2gmx to
>     join them head to tail (using the residue number field to indicate
>     the breaks, and the name to match up with the topology you've
>     defined), and you may then need either terminating residues of a
>     different name or a .tdb entry.
> 
> 
>         I dont think it is a visualisation artefact, because it really
>         gives less number of bonds, corresponding to the missing
>         intermonomeric bonds.
> 
> 
>     Your visualization software is not reading a file format that is
>     encoding any topology (since you haven't produced one yet). Thus
>     it's inventing some bonds based on the coordinates. The output of
>     pdb2gmx that contains topology information is the .top file, not the
>     coordinate file.
> 
> 
>         Should I do now both (introducing a chain identifier in the pdb,
>         but how?, and defining the intermonomeric bonds via dummy in the
>         pdb and tdb?)?
> 
> 
>     I suppose there are some circumstances where chain identifiers might
>     be useful, but since you haven't even told us what your monomer and
>     system are, it's hard to help you.
> 
> 
>     Mark
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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