I have used the following input:
parm complex.prmtop
trajin produc.nc
hbond donormask :14 acceptormask :18&!.H avgout hoogsteen.dat
hbond donormask :14 acceptormask :18&!.H dist 3.5 angle 135.00 avgout
hoogsteen_o.dat
Is this right to calculate the percentage hoogsteen bond occupancy?
On Sat, Feb 29, 2020 at 11:43 AM Sruthi Sudhakar <
sruthisudhakarraji.gmail.com> wrote:
> Respected group members,
>
> If someone is working in the G quadruplex- ligand simulations, could you
> please tell me how to obtain the percentage hoogsteen bond occupancy
> between the dG residues with each quartet? Since I am a beginner I am not
> familiar about the inpuit for this.
> Thanking you in advance.
> Sruthi Sudhakar
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 29 2020 - 01:30:02 PST
