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.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.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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Received on Fri Dec 05 2008 - 10:32:52 PST
