Re: [AMBER] ask for help

From: m13654940810 <>
Date: Fri, 19 Sep 2014 10:39:58 +0800

In fact,I replaced multipole type "None" with "Z-then-X" for Na+,which is required to make prmtop file.
I don't think it's OK for the value of the "FLAG CHARGE"


发件人:Jason Swails <>
发送时间:2014-09-19 10:06
主题:Re: [AMBER] ask for help
收件人:"AMBER Mailing List"<>

On Thu, Sep 18, 2014 at 9:18 PM, m13654940810 <> wrote:

> Hello,Amber community
> I want to use amoeba force field to run MD with AMBER14,but I wonder if
> there is something wrong with my prmtop file.
> A DNA pdb file was prepared with tleap command in AMBER14.
> like this:
> tleap -s -f leaprc.ff99bsc0
> B=loadpdb ***
> check B
> solvatebox B TIP3PBOX 8.0
> addions B Na+ 0
> savepdb B B.pdb
> I wrote down the box information(a-axis,b-axis,c-axis) for the Key file.
> Next,I used pdbxyz in tinker6.3v to convert it into and used
> to reproduce a new pdb file B.pdb_2 as the input of tinker_to_amber.
> The key file :
> paramters ***/amoebabio09
> a-axis ***
> b-axis ***
> c-axis ***
> Then,analyze was used to produce B.analout:
> analyze B PC > B.analout
> In B.analout,I replaced multipole type "None" with "Z-then-X".

​Why? It seems to me like you are rather arbitrarily changing the force
field (which in general is not a good idea).

> Finally,I used tinker_to_amber to produce inpcrd and prmtop files:
> tinker_to_amber -name B -title "B Amoeba FF"
> In the prmtop file,I found that numbers are zero under the "FLAG CHARGE"
> term.

​AMOEBA uses a point multipole expansion for each atom -- permanent
monopoles (these are the charges), dipoles, and quadrupoles (and then there
is an induced dipole). The mulitpole moments for each of the atoms is in
the AMOEBA_LOCAL_FRAME_MULTIPOLE​S_LIST. There are 10 (potentially unique)
multipole terms for each atom -- the monopole, 3 dipole components, and 6
quadrupole components.

In fact, most of the standard fields used in the prmtop file for more
traditional force fields are completely ignored when using the amoeba force
field. All of the parameters will be defined in sections that start with


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 18 2014 - 20:00:05 PDT
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