Dear amber users,
How to do MM-PBSA calculation in different temperature other than 25 or 298
K?
On Tue, Oct 25, 2016 at 1:59 PM, shahab shariati <shahab.shariati.gmail.com>
wrote:
> Dear Adrian,
>
> I did md simulation in temperature = 340 K using following in file:
>
> ------------------------------------------------------------
> ------------------------
> prod1_complex_solvated
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=2500000,dt=0.002,
> cut=10.0,ntb=2,ntp=1,taup=2.0,
> ntc=2,ntf=2,
> ntpr=2500,ntwx=2500,
> ntt=3,gamma_ln=2.0,
> temp0=340.0,
> /
> ------------------------------------------------------------
> ------------------------
>
> I want to do mmgbsa calculation in temperature = 340 K.
>
> I used following input file:
>
> ------------------------------------------------------------
> ------------------------
> Input file for running PB
> &general
> startframe=10, endframe=4000, interval=100,
> verbose=1, keep_files=1,
> entropy=1,
> ntt=3,gamma_ln=2.0,
> temp0=340.0,
> /
> &gb
> igb=2, saltcon=0.100,
> /
> ------------------------------------------------------------
> --------------------------
>
> But, I encountered with
>
> InputError: Unknown variable ntt in &general
> Enter `MMPBSA.py.MPI --help` for help
> ------------------------------------------------------------
> --------------------------
>
> How to change the temperature in mmgbsa?
>
> How to resolve this problem?
>
> On Fri, Sep 23, 2016 at 5:33 PM, shahab shariati <
> shahab.shariati.gmail.com> wrote:
>
>> Dear Adrian,
>>
>> Thanks for your quick answer.
>>
>> I will use the following in file for MM-PBSA calculation:
>>
>> ------------------------------------------------------------
>> -----------------
>> Input file for running PB
>> &general
>> startframe=10, endframe=4000, interval=100,
>> verbose=1, keep_files=1,
>> entropy=1,
>> /
>> &gb
>> igb=2, saltcon=0.100,
>> /
>> &pb
>> istrng=0.100,
>> /
>> ------------------------------------------------------------
>> ------------------
>>
>> For different temperatures, should I use "temp0=310.0" in the &cntrl
>> namelist like what is in the in file for MD?
>>
>> ------------------------------------------------------------
>> ------------------
>> prod1complex_solvated
>> &cntrl
>> imin=0,irest=1,ntx=5,
>> nstlim=2500000,dt=0.002,
>> cut=10.0,ntb=2,ntp=1,taup=2.0,
>> ntc=2,ntf=2,
>> ntpr=2500,ntwx=2500,
>> ntt=3,gamma_ln=2.0,
>> temp0=310.0,
>> /
>> ------------------------------------------------------------
>> -----------------
>>
>> Best regards,
>> Shahab
>>
>> On Fri, Sep 23, 2016 at 4:15 PM, Adrian Roitberg <roitberg.ufl.edu>
>> wrote:
>>
>>> Technically yes, you have to RERUN the MD at the new temperature and
>>> rerun mmpbsa. You should not reuse the MD at 298 and simply change the
>>> temperature in mmbpsa.
>>>
>>> However, it is extremely unlikely that you will see statistically
>>> meaningful differences between 298 and 310 with mmbpsa.
>>>
>>> Adrian
>>>
>>>
>>>
>>> On 9/23/16 7:07 AM, shahab shariati wrote:
>>> > Dear amber users,
>>> >
>>> > I want to calculate the binding free energy of several protein-ligand
>>> > complexes in two temperatures 298 and 310 K using MMPBSA.py in
>>> Ambertools
>>> > 14.
>>> >
>>> > Can I do that (My main question is about the temperature)?
>>> >
>>> > Any help will highly be appreciated.
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> --
>>> Dr. Adrian E. Roitberg
>>> University of Florida Research Foundation Professor.
>>> Department of Chemistry
>>> University of Florida
>>> roitberg.ufl.edu
>>> 352-392-6972
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
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Received on Wed Oct 26 2016 - 11:30:02 PDT
