Re: [AMBER] Amoeba with water and ion

From: Xioling Chuang <>
Date: Sun, 19 Jun 2011 16:49:18 +0200

Dear All,
I have several questions concerning the Amoeba force field.
1. Is there any tutorial for the use of amoeba force field?
2. When I started sleap, then followed by command "source leaprc.amoeba", I got error message.
% sleap
[gtkleap]$ source leaprc.amoeba
loadamoebaparams amoebapro09v4.prm
sleap: ambfrc-amoeba.cpp:35: void mort::ambfrc::amoeba::read_atom(std::basic_istream<char, std::char_traits<char>> &, mort::molecule_t &, mort::molecule_t &): Assertion `atomid==atomff.natom()+1' failed.
Why was it failed? I also tried to copy all files concerning amoeba database to the working directory, I obtained the same error. But when I replace "amoebapro09v4.prm" with "amoebapro.prm" for loadamoebaparams, there was no error message. Should I use amoebapro.prm instead?
3. In leaprc.amoeba, there is no library or parameter file called by amoeba (only amino acid is called). Can amoeba be used for nucleic acids? If yes, what library file should be load?
4. I found in $AMBERHOME/AmberTools/test/sleap/amoeba that one uses "solvatebox unit WATBOX 8.0" to solvate the solute with water (i.e. the name of water model is WATBOX). However, there is no an example for adding ions. If I want to add Na+ ions, what command and what ion name must be used? I tried with "addions unit Na+ 10" or "addions unit NA 10", but sleap does not recognize neither Na+ nor NA. Should I load parameter file of ions first? If yes, which file?
Thank you very much in advance for your answers for the long list of questions.
> >
> > As I understand, Amoeba force field has it own parameters for water and
> > ions. If I want to use Amoeba for MD simulation of the system solvated
> > in water and ions, should I use the common command like,
> > - solvatebox dna TIP3PBOX 8.0
> > - addions dna Na+ 0
> > Also, should I load frcmod for TIP3P and for ions?
> If you want to use the Amoeba force field, you need to use its parameters for
> water and ions, *not* TIP3 water. Of course, you are certainly allowed to
> experiment with whatever force field combination you like, but I don't think
> what you propose is likely to yield results of very much interest.
> ...dac
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Received on Sun Jun 19 2011 - 08:00:04 PDT
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