AMBER Archive (2008)

Subject: Re: AMBER: Input file for Minimization

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Feb 11 2008 - 11:06:42 CST

just to clarify- I think Ross means that _implicit_
solvent is slow for 200AA, and use explicit (he
said explicit for both)

On Feb 10, 2008 1:55 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
>
> Hi Patrick,
>
> This really depends on what you mean by the term minimize and what you want
> to do with the resulting structure. Note the file below will certainly
> minimized your structure (in implicit solvent) however it will only take you
> to the nearest local minimum which will mean you won't get much change in
> structure. If you want to explore more of the local phase space then you can
> try simple simulated annealing and then cooling down to zero K. Beyond that
> you will have to start looking in to procedures like replica exchange or
> other more complex approaches.
>
> The minimization from the tutorial you are referring to was purely to "clean
> up" the structure prior to running molecular dynamics on the system.
>
> Also note that a 200aa protein in explicit solvent is going to be very slow,
> you are probably better doing things in explicit solvent.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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>
>
>
> ________________________________
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Campbell, Patrick
> Sent: Saturday, February 09, 2008 13:19
> To: amber_at_scripps.edu
> Subject: AMBER: Input file for Minimization
>
>
>
>
> Hello All,
>
> I would like some information concerning the parameters to set for a
> minimization of a 200 aa, 30 kD protein. I was following from the AMBER
> tutorial by Ross Walker, and was wondering if the min1.in file which he
> quotes from the Simmerling, Strockbine and Roitberg paper could be modified
> for this process.
>
> min1.in
>
> Stage1 - minimisation of TC5b
> & cntrl
> imin=1, maxcyc=1000, ncyc=500,
> cut=999., rgbmax=999., igb=1, ntb=0,
> ntpr=100
> /
>
> If this file could be modified, could you suggest some parameters for this
> process.
>
> Thanks again for all your help.
>
> Pat
>
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