As previously suggested read through section 29.1 of the manual. Then
sections 29.11.1 and 29.11.2 show an actual example, including an
example for torsional angle.
Also tutorial 7.5 (section 2) on Amber tutorails has example for how to
do torsional restraints.
https://ambermd.org/tutorials/advanced/tutorial17/section2.php
To give you sense of what numbers you might need to put and to better
understand these restraints overall, take a look at the detailed
description of restraint variables here:
https://ambermd.org/Questions/constraints.html
If you're still having issues after having looked through all this, feel
free to ask questions.
Solen
On 2/18/2025 2:09 PM, Devid Sahu via AMBER wrote:
> Thank you for your response. I have simulated a system, but now I want to
> apply a dihedral restraint at 180 degrees. I understand that I need to
> specify the angle, force constant, and other parameters, but I am unsure
> how to determine their values and how to incorporate them into the prod.in
> file.
> *prod.in <http://prod.in/>: *
> Production
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 8.0, ntr = 0,
> ntc = 2, ntf = 2,
> temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 400000000, dt = 0.002,
> ntpr = 100000, ntwx = 100000, ntwr = 10000,
> iwrap=1,
> ig=-1
> &rst
> iat=126,127,128,129,
> r1= ??, r2=??, r3=??, r4=??,
> rk2=??, rk3=??,
> &end
> /
> Any suggestions or guidance would be highly appreciated.
> Thanks
>
> On Tue, Feb 18, 2025 at 10:45 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> can you clarify what you need? Do you have a working simulation in Amber,
>> and just need to know the restraint format? or are you wanting to learn how
>> to do all of the simulation input?
>> section 29.1 of the Amber24 manual gives information on how to set up the
>> distance, angle and dihedral restraints.
>> also, have you looked at the tutorials at https://ambermd.org/tutorials/?
>> They can help you get started.
>>
>>
>>
>> On Tue, Feb 18, 2025 at 1:04 AM Devid Sahu via AMBER <amber.ambermd.org>
>> wrote:
>>
>>> Dear users
>>> I am looking to simulate an organic molecule with 208 atoms and need to
>>> apply restraints on two dihedral angles to a value 180 . I have explored
>>> some online resources but still lack clarity on how to specify the angles,
>>> atoms, and force constants. Could someone briefly guide me on the script
>>> and submission process? Forgive me as I am new in this field.
>>>
>>> Many thanks!!
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
> _______________________________________________
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Received on Tue Feb 18 2025 - 14:00:02 PST
