Hi,
Just some general advice - you are better off upgrading to the latest
version of AmberTools/Cpptraj (14,
http://ambermd.org/AmberTools14-get.html) before attempting any
calculation. Version 13 is quite out of date at this point.
-Dan
On Fri, Sep 5, 2014 at 12:06 PM, MOHD HOMAIDUR RAHMAN
<rahmanhpu.gmail.com> wrote:
> Dear Jason
>
> Thank you for help
>
>
>> Dear Amber Users
>> I want to calculate interaction energy between two urea molecules in
>> homogeneous urea solution (only urea molecules are there). For that I used
>> antechamber modules to generate urea "prep" and "frc" file. The generated
>> file contain GAFF force field parameter. After production MD run, I
> process
>> the trajectory to calculate pairwise interaction energy. I used the
>> pairwise command but I am getting + 36.34 kcal/mol while the reported
>> theoretical value for dimer is -10.33 kcal/mol (MP2/aug-cc-pVDZ).
>>
>> I am using "CPPTRAJ: Trajectory Analysis. V13.0".
>>
>
> What's the actual command you're using? (Not just the command name, the
> _full_ command).
>
> I am using the following command
>
> cpptraj -p urea.top -i pairwise.in
>
> In pairwise.in
>
> trajin ../md_file/
> md1
> .crd
>
> reference ../md_file/urea
> _leap
> .crd
>
> pairwise U_U :URA out pairwise_
> IE
> .txt cuteelec 12.0 cutevdw 12.0
>
>
> Is there are bugs in this command??
>>
>
> cpptraj is part of Amber. Amber has no bugs. So cpptraj has no bugs.
>
> Kidding, of course, but in cases like this I've found that it's best to
> assume I don't fully understand what I'm computing or exactly what I asked
> the program to compute. This is why knowing the exact command is important.
>
> Also, there's no reason to expect that two urea molecules in bulk urea have
> the same interaction as the urea dimer... You're also comparing a minimum
> energy structure (MP2/aug-cc-pVDZ) with what is likely an ensemble property
> if you're computing this value over a trajectory. When doing comparisons
> like this, it's very important that you make every effort to make sure you
> are making a fair comparison.
>
> The main point is that, How urea interaction energy showing positive value
> ?
> It means that the system is thermodynamically very unstable due to positive
> interaction energy (unfavorable interaction). The value should be equal to
> zero
> or below zero in any range (never exactly match with quantum calculation)
> because we are calculating over trajectory.
>
> Or may be the high positive Interaction value arise due to wrong non-bonded
> parameter.
>
> Thanks
> Rahman
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Sep 05 2014 - 20:00:03 PDT
