Hello Dan
Indeed it does and as was was asked to do this to helt a colleague working with NMR on a large set of samples, it will defiantly come in handy at a later point in time.
Super grateful for you feedback and a big thank you to both! Have a fantastic weekend
// Gustaf
> On 3 Oct 2019, at 21:33, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> I know I'm late to respond here, but you could use the
> 'permutedihedrals' command in cpptraj to generate a pseudo-trajectory
> with a dihedral rotated at regular intervals, then use 'crdaction
> <COORDS> energy' to get the energy. Something like:
>
> parm <topology>
> loadcrd <single frame> name MyCrd
> permutedihedrals crdset MyCrd resrange 7 interval 30 phi crdout Rotate
> crdaction Rotate energy out Rotate.energy.dat
> quit
>
> This will create a pseudo-trajectory named Rotate by rotating around
> residue 7 phi by 30 degrees, then calculate the energy of that pseudo
> trajectory. See the manual for full details on the commands.
>
> Hope this helps,
>
> -Dan
>
> On Thu, Sep 26, 2019 at 6:14 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>> Thank you very much Karl
>>
>> This is a very good start and I’ll look into it. At this point I’m just interested in qualitative results, "is there an apparent barrier or not". The actual numbers are of less importance right now and if needed I’ll probably turn to some QM calculations.
>>
>> Best regards
>> // Gustaf
>>
>>> On 26 Sep 2019, at 09:48, Karl Kirschner <k.n.kirschner.gmail.com> wrote:
>>>
>>> Hello Gustaf,
>>>
>>> The way that I know is to use a restraint file to specify the dihedral
>>> angle and constraint forces. In the following example (using a filename of
>>> 02.rest), I have constrained atoms 1-5-8-11 to an angle of 30.0 degrees
>>> using a force of 30000.0 :
>>>
>>> &rst iat = 1, 5, 8, 11,
>>> r1 = 29.0, r2 = 30.0, r3 = 30.0, r4 = 31.0,
>>> rk2 = 30000.0, rk3 = 30000.0,
>>> &end
>>>
>>> Then within the min.in file you need to refer to this file:
>>>
>>> Gas-Phase Constraint Minimization
>>> &cntrl
>>> imin=1, dielc=1,ntb=0,
>>> maxcyc=20000,ntxo=1
>>> drms=0.01,nmropt=1,
>>> cut=40.0,
>>> &end
>>> &wt type='END' &end
>>> LISTOUT=POUT
>>> DISANG=02.rest
>>>
>>> Of course if you using a good input structure (by specifying it in leap to
>>> create the coordinate file for running the minimization) for each angle
>>> that you are wanting to model, you will ensure better results. The example
>>> that I give is for a gas-phase, so you will need to consider if and how to
>>> include solvation effects.
>>>
>>> Best regards,
>>> Karl
>>>
>>> Karl. N. Kirschner, Ph.D.
>>> Research Associate
>>> Department of Computer Science
>>> University of Applied Sciences Bonn-Rhein-Sieg
>>> Grantham-Allee 20, 54757 Sankt Augustin, Germany
>>> Twitter: .k_n_kirschner <https://twitter.com/k_n_kirschner>
>>>
>>>
>>> On Thu, Sep 26, 2019 at 8:30 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>>
>>>> I was curious if anyone has experience with calculating rotational/torsion
>>>> energy over a single bond using amber? I am looking for a smooth way to get
>>>> an indication of potential energy barriers and an estimate of the size.
>>>>
>>>> If anyone knows of any tutorials or online resources describing the
>>>> process I’d greatly appreciate some tips.
>>>>
>>>> Best regards
>>>> // Gustaf
>>>>
>>>>
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Received on Thu Oct 03 2019 - 23:30:02 PDT
