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 Mar 18 2019 - 04:00:02 PDT
