Re: [AMBER] Amoeba with water and ions (2)‏

From: David A Case <>
Date: Tue, 21 Jun 2011 09:20:20 -0400

On Tue, Jun 21, 2011, Xioling Chuang wrote:
> 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.
> Abort

I can reproduce this problem, and we are looking into it.
> 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?

We don't have the files needed for nucleic acids in Amber yet. You might
contact Pengyu Ren.

I agree that a tutorial for amoeba would be great. You may have to learn how
to do things in Tinker, then try to apply the same ideas to Amber.


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Received on Tue Jun 21 2011 - 06:30:03 PDT
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