AMBER Archive (2008)

Subject: Re: AMBER: Minimisation and heating under GB conditions

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Nov 03 2008 - 08:17:34 CST

I forgot to ask about restraints. I have a transmembrane protein and a
peptide docked on it on the extracellular portion. I rnounced to set
the lipidic membrane for obvious reasons of computational cost. Is it
possible, from this vague description, imagine where to put restraints
during minimization (although the GB environment seems to have kept
the residues in order, as I start from scratch more care may not be
useless)
Thanks
francesco

On Mon, Nov 3, 2008 at 3:01 PM, David A. Case <case_at_biomaps.rutgers.edu> wrote:
> On Mon, Nov 03, 2008, Carlos Simmerling wrote:
>>
>> also I STRONGLY recommend against igb=1. we've published several
>> papers (as have others) showing that this is not a good option. I
>> recommend igb=5 and mbondi2 radii.
>
> Just a (somewhat off-topic) note: the comments above are based on studies on
> proteins. For nucleic acids, we have less extensive study, but igb=1 is
> likely to still be a viable option there.
>
> ...dac
>
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