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 Tue Oct 25 2016 - 03:30:03 PDT
