Re: [AMBER] Help about the igb

From: Elaine Cheung <>
Date: Mon, 27 Aug 2012 23:22:50 +0800 (CST)

Thank you for your help.


At 2012-08-25 06:55:27,"Carlos Simmerling" <> wrote:
>In water? peptide secondary structures are difficult to get quantitatively
>right using most current GB models- these is fairly well documented in the
>literature. Whether these will work for you depends on whether you're
>looking for qualitative or quantitative answers. igb=5 is perhaps the best
>choice in Amber among the GB models that are published, though it does
>overstabilize helices; I think igb=8 is significantly better but we're
>still preparing a manuscript that describes all of the details so at the
>moment it's probably best used by experts.
>My opinion is that the manual, archives and email list are great places to
>go to find out about how to best use Amber, and what the various options
>do. For actually deciding what types of simulations you *should* do,
>however, I often tell people that the peer-reviewed literature is the place
>to go. If you don't have enough experience on your own to know what type of
>simulation will suit your needs, the best option by far is to read articles
>that were trying to answer questions similar to your own, and see what they
>did to successfully answer them. Then, you can ask here or other places to
>find out how you might implement this kind of simulation.
>On Aug 22, 2012 9:52 PM, "Elaine Cheung" <> wrote:
>> 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" <>
>> wrote:
>> >What are you trying to learn?
>> >On Aug 22, 2012 1:57 PM, "Elaine Cheung" <> 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 Mon Aug 27 2012 - 08:30:03 PDT
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