Hello again,
I think this is something that you have to decide for yourself. I know
that there are capping residues for DNA and RNA included in Amber's library
files, so you might want to look into that. Ultimately, the goal of
creating any computational model is to mimic the real system, which you
want to do to the best of your abilities while weighing in several factors
(e.g. resources, time, availability of code). Thus, you should use capping
residues that are also seen experimentally. If you decide not to do that,
then rationally choose a capping residue that you believe will introduce
little error into your MD observables. The same goes for what parameters
you choose to use. At the end-of-the-day, you will want to provide
supporting evidence for what you choose, and clearly state how you made the
model so that it is transparent to the community.
I hope this helps.
Cheers,
Karl
On Thu, Apr 2, 2015 at 4:08 PM, James Starlight <jmsstarlight.gmail.com>
wrote:
> 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > --
> > Karl. N. Kirschner, Ph.D.
> > Research Associate
> > Bonn-Rhein-Sieg University of Applied Sciences
> > Grantham-Allee 20, 54757 Sankt Augustin, Germany
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Apr 02 2015 - 08:00:02 PDT
