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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>>
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Received on Thu Aug 07 2014 - 10:30:02 PDT
