If anyone has any input, it would be greatly appreciated.
On Wed, May 10, 2023 at 11:26 AM Prithviraj Nandigrami <
prithviraj.nandigrami.gmail.com> wrote:
> Dear AMBER Experts and Users,
>
> I am trying to calculate native contacts for a nucleic acid over an MD
> trajectory. Can someone please guide me how to specifically calculate the
> "stem loop" contacts using cpptraj? What should be the appropriate "mask"
> selection for this purpose?
>
> Below is the reference script to calculate native contacts:
>
> parm input.strip.parm7
> trajin input.strip.nc
> autoimage
> nativecontacts name NC1 :1-47&!.H= \
> writecontacts native-contacts.dat \
> resout resout.dat \
> distance 3.0 \
> byresidue out all-residues.dat mindist maxdist \
> map mapout gnu \
> contactpdb contactspdb.pdb \
> series seriesout native-contacts-series.dat
> run
> lifetime NC1[NC] out lifetime.dat
> run
>
> Any help would be much appreciated.
>
> Best,
>
> PN
>
>
>
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Received on Fri May 12 2023 - 13:00:02 PDT
