[gmx-users] Re: Force field for polymer molecule - tips (Mark Abraham)

[Justin A. Lemkul]

Jernej Zidar wrote:
> Hi Mark.
>>> How will pdb2gmx "know" it has to parse the monomeres.rtp file?
>> It can't. You must add to an existing .rtp file.
> 
> That's a problem (and a negative surprise), because I can't just add a
> new residue to the aminoacids.rtp in Charmm27.ff folder. Charmm27 and
> CGenFF are two different things, though they can be used together.
> 

The CGenFF files can be found on the Gromacs website:

http://www.gromacs.org/Downloads/User_contributions/Force_fields

To make them fully functional and capable of using pdb2gmx, you would have to 
add several files - .rtp, .hdb, .atp, and probably a few others.

>> I will add that you will also have to add the residue to aminoacids.dat
>> file, so that the polymer repeat unit is recognized. for your small
>> polymer molecule you can just generate from the swissparam website
> 
> That could well work in the case of the smallest polymer that is
> composed of just five monomers, but it is absolutely out of the
> question in the case of experimentally-relevant polymers that are
> composed of at least 40 units.
> 

How many different monomers are involved?  Repeat units and polymeric assemblies 
are precisely what pdb2gmx is for (consider the trivial example of a protein). 
For further polymer-related tips, see the following:

http://www.gromacs.org/Documentation/How-tos/Polymers

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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