Hi Karl and thank you for information!
one question: what caps should I use from leap for the non-peptide
monomer- actually I'm working with some nucleotide-acid derivative (i
think ace and nh2 is not valid here). Should I provide only capped
dimmer for the amber parmcheck to restore all missed params from the
structure?
Regards,
James
2015-04-02 15:23 GMT+02:00 Karl Kirschner <k.n.kirschner.gmail.com>:
> Hello James,
>
> The first thing you will need to do is to define three residues: 1) one
> for the capping the polymer at the "head", 2) one for capping the polymer
> at the "tail", and 3) one for all residues in the middle. (Depending on how
> you set up the residue files, you might need to define the head and tail
> atom for each of the residues, using leap's set command.) Then use the
> sequence command to put it all together. Make sure that the residue files
> (prep or mol2) have different residue names, which is important for the
> sequence command.
>
> If you wish to make a periodic boundary box, then define a solute and
> solvent molecule. In this case both the solute and solvent will be the same
> molecule. Finally, build the PBC box.
>
> I did this awhile ago for PMMA. Below is a representative sequence of
> commands that should illustrate what I wrote above. This creates a very(!)
> artificial model. Thus, make sure you equilibrate they system, which can be
> difficult and time consuming that depending on the length of your polymer.
> I would recommend looking at some literature (e.g. Dr. Florian
> Müller-Plathe) that simulates polymer melts to see how they ensured
> reasonable polymer geometries and entanglements. I think the state-of-art
> concerning this is to do some coarse graining, followed by backmapping to
> atomistic space and further simulations.
>
> Bests,
> Karl
>
> -----
> source ~/leaprc.polymer
>
> loadAmberPrep POL_head.prep
> loadAmberPrep POL_middle.prep
> loadAmberPrep POL_tail.prep
>
> poly = sequence {BEG MID MID MID END}
>
> solv = sequence {poly}
> mol = sequence {poly}
>
> solvateDontClip mol solv 12.0
>
> saveamberparm poly polymer_leap.top polymer_leap.crd
> savepdb poly polymer_leap.pdb
> ----
>
>
> On Thu, Apr 2, 2015 at 2:41 PM, James Starlight <jmsstarlight.gmail.com>
> wrote:
>
>> Dear Amber users!
>>
>> I need to build long polymer consisted of several monomers and make
>> all input files for amber simulation. Here monomer is some
>> non-standart residue for which I also have force field parameters (in
>> amber-accept form) made by external software. I'd be very thankful if
>> someone provide me with the suggestions how it could be done using
>> xleap or alternatively another software.
>>
>>
>> Regards,
>>
>> James
>>
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>>
>
>
>
> --
> Karl. N. Kirschner, Ph.D.
> Research Associate
> Bonn-Rhein-Sieg University of Applied Sciences
> Grantham-Allee 20, 54757 Sankt Augustin, Germany
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Received on Thu Apr 02 2015 - 07:30:03 PDT
