sounds good. Thanks Dave and Ross for the help :)
Mohammad
On Aug 7, 2014, at 11:23 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Mohammad,
>
>
> As Dave Case said the 180 offset here gives you minima at 0 and 180 (since
> the periodicity is 2) - hence it works to favor both the cis and trans
> configurations. Best thing to do is plot the equation with those values
> and you'll be able to see it better.
>
> All the best
> Ross
>
> On 8/6/14, 9:47 PM, "Mohammad Salem" <mohammad.alaraby.gmail.com> wrote:
>
>> 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 can©öt 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 Thu Aug 07 2014 - 12:30:02 PDT
