Re: [AMBER] Improper torsions in NMA

From: FyD <>
Date: Fri, 06 Mar 2015 09:02:49 +0100

Dear Ganesh,

> I know I am supposed to ask AMBER questions on the forum. But this is a
> question on impropers. In fact I did ask on AMBER forum and I am still
> unclear regarding the improper torsions in NMA.
> Could you please help ?

ok - but please next time please re-post in the Amber mailing list.

> HC3 H HC3
> \ | /
> HC3-C3 - N - C - C3 - HC3
> / || \
> HC3 O HC3
> Why does AMBER and when they convert to GROMACS consider only 1 improper
> C-C3-N-H

- Amber defines impropers for sp2 system center
- the presence of an improper is not mandatory to create the
prmtop/prmcrd files
   (i.e. an improper can be 'missing')
- some sp2 centers do not have improper (user defined): such as sp2
centers between 2 cycles

> and C3-N-C-O when there should be three each or six in total. Are the
> others same values?
> gaff
> X -X -c -o 10.5 180. 2. JCC,7,(1986),230
> but when they are using NMA with AMBER parameters in GROMACS, they use only
> C3-N-C-O.
> How about N-O-C-C3 and C3-O-C-N.

in the parm99.dat file the improper section starts by:
X -X -C -O 10.5 180. 2. JCC,7,(1986),230
and ends by:
C -CT-N -O 1.1 180. 2. Junmei et al.1999

the improper center is at the third position; the order of the three
other is NOT controlled.

the code search first for a specific parameter (i.e. without X) and if
not found search for a generic parameter (i.e. with X) and if not
found report a warning (not an error) about a missing improper

for NMA you could define 2 impropers for the N sp2 and the C sp2 centers

N sp2: specific (found)
C -CT-N -H 1.1 180. 2. Junmei et al.1999
X -X -N -H 1.0 180. 2.
  is not used; I guess - just check the prmtop using the proper tool

C sp2: generic
X -X -C -O 10.5 180. 2. JCC,7,(1986),230

Concerning Gromacs better asking to the Gromacs mailing list...

I am sure people from the Amber mailing list can correct/complete my email...

regards, Francois

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Received on Fri Mar 06 2015 - 00:30:02 PST
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