[AMBER] Amoeba with water and ions (2)

From: Xioling Chuang <xioling_c.hotmail.com>
Date: Tue, 21 Jun 2011 04:05:48 +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
loadoff amoeba_amino.off
loadoff amoeba_aminont.off
loadoff amoeba_aminoct.off
loadoff amoeba_watbox.off
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 for amoeba 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.
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Received on Mon Jun 20 2011 - 19:30:03 PDT
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