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 - 06:30:08 PDT
