Hello Mishra,
To be ramachandran's consistent (-180 to +180).
Greeting,
Hector.
> Many thanks. Then what is the range of dihedral angle (-180 to 180 or 0 to
> 360) it would dump to the file ? Is there someway I can restrict output
> angles to be written between -180 to 180 or 0 to 360 ?
>
> Thanks,
> Mishra
>
> On Thu, May 12, 2016 at 11:05 PM, David Cerutti <dscerutti.gmail.com>
> wrote:
>
>> In my experience it does not matter; you can even specify angles beyond
>> 360
>> and it will re-image them as needed.
>>
>> On Thu, May 12, 2016 at 9:58 AM, mish <smncbr.gmail.com> wrote:
>>
>> > Dear all,
>> >
>> > I am running umbrella sampling simulations using pmemd (cuda) from
>> > Amber14. In these calculations I want to construct PMF for rotating a
>> > dihedral angle of an molecule by 360 degree. I am am slightly confused
>> over
>> > the range of input dihedral angle in input "DISANG" file. Should it be
>> from
>> > -180 to 180 or from 0 to 360. One of the calculations went with 0 to
>> 360
>> > but in another one I am getting negative values (between 10 and -10)
>> dumped
>> > for window at 0 degree. Should I simply convert them between 0 and 360
>> and
>> > construct PMF ? Example file disang.270 is as follows :
>> >
>> > -------------
>> >
>> > harmonic restraints for 270 deg
>> >
>> > &rst
>> >
>> > iat=2913,2915,2918,2932,
>> >
>> > r1=210.0, r2=270.0, r3=270.0, r4=330.0,
>> >
>> > rk2=200, rk3=200,
>> >
>> > &end
>> >
>> >
>> > Best,
>> >
>> > Mish
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--------------------------------------
Dr. Hector A. Baldoni
Profesor Adjunto (FQByF-UNSL)
Investigador Adjunto (IMASL-CONICET)
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 12 2016 - 17:00:02 PDT
