I am trying to learn about the secondary structure of the peptide by using SMD method.
At 2012-08-22 17:28:26,"Carlos Simmerling" <carlos.simmerling.gmail.com> wrote:
>What are you trying to learn?
>On Aug 22, 2012 1:57 PM, "Elaine Cheung" <playbutplay.126.com> wrote:
>
>> Hi,
>> I am trying to build a system of gp41 peptide by using force field ff99SB
>> and ff12SB under surface area. I use the command "set default PBradii
>> mbondi2" to prepare the prmtop file. But I don't know which value I should
>> choose for igb in the mdin file, igb=2 or igb=5? Which one is better for
>> the force field ff99SB and ff12SB?
>>
>>
>> Best,
>> Elaine
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Received on Wed Aug 22 2012 - 19:00:03 PDT
