[gmx-users] Re: gmx-users Digest, Vol 92, Issue 73

[Jernej Zidar]

Hi Justin.
  I am now trying to generate all the missing files (.rtp, .hdb, .tdb,
.atp). I will present the monomeres as aminoacids. Since the polymer
will be simulated along with a lipid membrane (CHARMM36 force field),
I won't actually need the aminoacids.

  I have five different monomers (3 + 2 terminal ones), that are quite
similar so after importing one I should be OK.

Best,
Jernej

On Wed, Dec 14, 2011 at 12:17,  <gmx-users-request at gromacs.org> wrote:
> 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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