Re: [AMBER] igb8 SURFTEN SURFOFF

From: Hai Nguyen <nhai.qn.gmail.com>
Date: Wed, 31 Jul 2013 16:03:57 -0400

Hi, please see my comment below


On Wed, Jul 31, 2013 at 4:33 AM, berin karaman <berinkaraman.yahoo.com>wrote:

> Dear Amber Users,
>
> I would like to ask which SURFTEN and SURFOFF parameters we should use for
> igb = 8 calculations for the protein systems ?
>
> We used the default values for surften (not sure what surfoff is) in our
paper
http://pubs.acs.org/doi/abs/10.1021/ct3010485

Since the nonpolar energy model in Amber is quite "simple" and has some
limitations, we decided not to systematically investigate the best value
for SURFTEN. However, with the default value, we were still able to
quantitatively reproduce the melting curves of several small proteins.


>
> Is there any recommended input parameters that we should specify in the
> input file for running igb = 8 ?
> And I couldnt also find what is the default values for SURFTEN and SURFOFF
> parameters implemented in AMBER for igb = 8?
>
>
The igb8 parameters were hard-coded in Amber so you don't need to specify
any special input, just using it like using igb = 2 or igb = 7. But we
recommend to use mbondi3 (specify in tleap input when you are building
topology file).

The default SURFTEN value is for ALL igb models.

I have read the manual and try to google and search the mailing list but
> couldnt find any statement about this issue. I may just missed it maybe but
> it would be very nice if you can comment on it.
>
> Thank you so much in advance.
>
> Best regards,
>
>
> Berin Karaman
>
>
>
>
> Medicinal Chemistry
> Institute of Pharmacy
> Martin-Luther-Universitšt Halle-Wittenberg
> Wolfgang-Langenbeck-Str. 4
> 06120 Halle (Saale), Germany
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>
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Received on Wed Jul 31 2013 - 13:30:02 PDT
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