Hi, thank you very much for the comments.
I would like to try the "Table:2 input parameters recommended for non polar solvation free energy calculations for protein systems" as it is given in the AMBER 12 / Examples/ TEMPLATE_INPUT_SCRIPTS / SURFTEN_SURFOFF_Recommendations.pdf file.
It would be very nice if you let me know how we can give the command in tleap/xleap for "Parse" and "Rmin" radii ? Is it also like "set default PBradii Parse/Rmin" ?
And how someone can change the MS=1 and IVCAP=1 or 5 in MMPSA.py input file ? I couldnt find it in general namelist variables for MS and IVCAP.
Best regards,
Berin Karaman
Medicinal Chemistry
Institute of Pharmacy
Martin-Luther-Universität Halle-Wittenberg
Wolfgang-Langenbeck-Str. 4
06120 Halle (Saale), Germany
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
To: berin karaman <berinkaraman.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, 31 July 2013, 22:03
Subject: Re: [AMBER] igb8 SURFTEN SURFOFF
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-Universität Halle-Wittenberg
>Wolfgang-Langenbeck-Str. 4
>06120 Halle (Saale), Germany
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Aug 01 2013 - 01:00:03 PDT
