AMBER Archive (2008)

Subject: Re: AMBER: Hybrid REMD amber10

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue May 20 2008 - 01:55:06 CDT

yes Ross is right- make sure even though you make an explicit solvent
prmtop that you choose the radii that you want for the GB part in leap.

On Mon, May 19, 2008 at 11:51 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi Geoff,
>
>
>
> Adrian or Carlos may be able to comment more definitively on this but I
> think this essentially means that the GB radii are required – obviously to
> do the hybrid part of the REMD – even though this is a solvated prmtop file.
> This should always be true since I believe leap always writes the radii to
> the prmtop file even if you solvated it. (%FLAG RADII)
>
>
>
> The key point though I think is that you need to consider what GB model you
> will use as part of the REMD when creating the prmtop file. I.e. if you plan
> to use GB=1 or 7 then you are fine with the defaults but if you want to use
> GB=2 or 5 then you need to execute 'set default PBradii mbondi2' in leap
> before saving the prmtop file.
>
>
>
> All the best
>
> Ross
>
>
>
>
>
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Geoff Wood
> Sent: Monday, May 19, 2008 5:42 AM
> To: amber_at_scripps.edu
> Subject: AMBER: Hybrid REMD amber10
>
>
>
> Dear Amber users,
>
>
>
> In amber10 the hybrid remd calculations have become a lot more
> user-friendly, which is great. However, in the manual it states "In
> particular this means that
>
> the correct GB radii must be specified in the fully solvated topology file,"
> I was wondering if anyone could elaborate on this?
>
>
>
> Thanks in advance.
>
>
>
> ----------------------------------------------------------------------------------------------------------------------------------
>
> Dr Geoffrey Wood
>
> Ecole Polytechnique Fédérale de Lausanne
> http://lcbcpc21.epfl.ch/Group_members/geoff/
>
> SB - ISIC - LCBC
>
> BCH 4108
> tel: +41 21 693 03 23
>
> CH - 1015 Lausanne
> e-mail: geoffrey.wood_at_epfl.ch
>
> ----------------------------------------------------------------------------------------------------------------------------------
>
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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