AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Nov 03 2008 - 12:52:23 CST

I'm not sure what you mean- restraints on temp? I meant positional
restraints turned off slowly (in stages)

On Mon, Nov 3, 2008 at 2:07 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> I finally imagined that you meant restraints on TEMP. This is the
> heatin that I'll use as soon as minimization is complete:
>
> heating gradually under GB conditions
> &cntrl
> imin=0, irest=0, ntx=1, ntb=0,
> igb=5, ntc=2, ntf=2,
> ntt=3, gamma_ln=2.0,
> nstlim=25000, dt=0.001,
> ntpr=500, ntwx=500,
> tempi=100.0, temp0=300.0,
> cut=999,
> nmropt=1
> /
> &wt TYPE='TEMP0', istep1=0, istep2=25000,
> value1=100.1, value2=300.0,
> /
> &wt TYPE='END'
> /
>
> On Mon, Nov 3, 2008 at 3:17 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>> 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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>>
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