Hi Johannes and Dr. Case,
May I ask if you have figured out which lines should be used as the c3-c3-os-c3 torsion parameter? I’m confused about this as well. It seems to me there’re two sets of parameters excluding the first line, one is for TorType=2, the other is for TorType=3. Could you also explain what does the TorType mean?
Thank you!
Best,
Lin
> On Mar 18, 2019, at 6:41 AM, Träg, Johannes <johannes.traeg.fau.de> wrote:
>
> Am 2019-03-15 20:20, schrieb David Case:
>> On Fri, Mar 15, 2019, Träg, Johannes wrote:
>>>
>>> I have a question regarding the assignment of GAFF2 parameters
>>> (gaff2.dat, Version 2.1, April 2016) to the dihedral angle
>>> c3-c3-os-c3.
>>>
>>> For this dihedral angle, the gaff2.dat file lists the following lines:
>>>
>>> X -c3-os-X 3 1.150 0.000 3.000
>>> JCC,7,(1986),230
>>>
>>> c3-os-c3-c3 1 0.240 0.000 -3 p29 GA
>>> c3-os-c3-c3 1 0.160 0.000 2 p29 GA
>>>
>>> c3-c3-os-c3 1 0.910 0.000 -3
>>> c3-c3-os-c3 1 1.000 0.000 -2
>>> c3-c3-os-c3 1 0.000 0.000 1
>>>
>>> Of course the fist line has to be omitted, since there are explicit
>>> entries for c3-c3-os-c3/c3-os-c3-c3. However, the .frcmod file
>>> prepared
>>> by parmchk2 lists the following lines:
>>
>> Can you say exactly what arguments you gave to parmchk2 to get this
>> result? Did you include the "-s 2" option? (cc-ing to Junmei for
>> comments as well.)
>>
> I used tha following command: parmchk2 -i ff.mol2 -f mol2 -o ff.frcmod
> -s 2 -a Y
>
>
>>>
>>> c3-c3-os-c3 1 0.240 0.000 -3.000
>>> c3-c3-os-c3 1 0.160 0.000 2.000
>>> c3-c3-os-c3 1 1.000 0.000 -2.000
>>> c3-c3-os-c3 1 0.000 0.000 1.000
>>>
>>> Finally, the .prmtop file prepared by leap contains only the values of
>>> theses lines:
>>>
>>> c3-c3-os-c3 1 0.240 0.000 -3.000
>>> c3-c3-os-c3 1 0.160 0.000 2.000
>>> c3-c3-os-c3 1 0.000 0.000 1.000
>>>
>>> Why is the line (1/0.910/0.000/2) missing in .frcmod? How (and why) do
>>> antechamber/leap choose the final values for the .prmtop file and not
>>> the lines (1/0.910/0.000/-3 1/1.000/0.000/-2) instead?
>>>
>>
>> ...dac
>>
>>
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Received on Mon Aug 05 2019 - 13:00:03 PDT
