Re: [AMBER] Question concerning a torsion parameter

From: Ross Walker <>
Date: Wed, 06 Aug 2014 18:42:58 -0700

Hi Mohammad,

If a dihedral is not explicitly specified with 4 atom types then leap will
look to see if there are any wildcards. In your case you identified the
correct wildcard which is indeed taken from parm10.dat. A quick check of
frcmod.ff12SB shows that nothing overrides this dihedral. So what you get

X -C -N -X 4 10.00 180.0 2. AA,NMA

Which actually translates to:

O - C -N -CX 1 2.5 180.0 2.

The barrier height of 10.0 is divided by 4 in the case of the wild card
(first integer) - this is because there are 4 dihedrals that would
typically match this wild card. If we consider a protein backbone we have:

  HC O 3C
  | | |
- CX- C - N - CX -
  | | |
  3C H HC

So in this case X - C - N -X matches:

CX- C -N -CX
CX- C -N -H
O - C - N -H
O - C -N -CX

None of which are overridden by explicit dihedrals in the parm10.dat file
or the frcmod.ff12SB file.

The diagram above is 2D but maps fairly well into 3D. In all cases the
dihedrals here are 180 degrees. You can see this better if you take a look
graphically in leap. Do:


source leaprc.ff12SB
foo = sequence { ACE ALA ALA NME }
edit foo

You will see that all those dihedrals are 180 degrees and so it is correct
for gamma to be 180 here.

All the best

On 8/6/14, 5:35 PM, "Mohammad Salem" <> wrote:

>Just to clarify: I am using ff12sb so I thought params are called from
>parm10.dat and frcmod12SB.
>waiting for your reply.
>On Aug 6, 2014, at 6:26 PM, Mohammad Salem <>
>> Hi All,
>> I am a bit confused on how the parameter for the dihedral angle: O -C
>>-N -CX is called from, say, PARM10.dat
>> I canšt find that exact torsion. What I can find is: X -C -N -X as
>> X -C -N -X 4 10.00 180.0 2. AA,NMA
>> Why is it then 180 and not 0?
>> Thanks in advance for your reply.
>> Regards,
>> Mohammad
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Received on Wed Aug 06 2014 - 19:00:02 PDT
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