AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Nov 04 2008 - 01:27:55 CST

I had forgot weight restraint (nmropt=1), which would have allowed the
temperature to raise to the final value abruptly.

As to positional restraints, in this case of a peptide docked onto a
large protein under GB conditions, I can't imagine where to restrain.
Perhaps some couple of atoms on the protein and peptide. Although I
can rely on previous observations that a drastic equilibration did not
distort the system, I have to study the manual better.

Thanks a lot for having guided me through the GB procedures.

francesco

On Mon, Nov 3, 2008 at 7:52 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> 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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