Hi Ross,
Thanks a lot for your reply and generous explanation. I am just confused about the CX-N-C-O dihedral. I can see all the others you mentioned are indeed 180, but this one I only see as zero. I might be looking at the wrong thing, so I attached a pic to look at.
What do you think?
Best regards and thanks again!
Mohammad
On Aug 6, 2014, at 7:42 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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
> is:
>
> 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:
>
> $AMBERHOME/bin/xleap
>
> 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
> Ross
>
>
> On 8/6/14, 5:35 PM, "Mohammad Salem" <mohammad.alaraby.gmail.com> wrote:
>
>> Just to clarify: I am using ff12sb so I thought params are called from
>> parm10.dat and frcmod12SB.
>>
>> waiting for your reply.
>>
>> thanks!
>> On Aug 6, 2014, at 6:26 PM, Mohammad Salem <mohammad.alaraby.gmail.com>
>> wrote:
>>
>>> 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
>>> follows:
>>>
>>> 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 - 22:00:03 PDT
