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

[Tsjerk Wassenaar]

Hi Jernej,

You can copy the charmm27.ff directory to your working directory and make
changes locally.

Cheers,

Tsjerk

On Dec 14, 2011 2:54 AM, "Jernej Zidar" <jernej.zidar at gmail.com> 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.

>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.

Jernej
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