Hello,
I was wondering if there is any update regarding this?
Thank you.
PN
On Tue, Jan 3, 2023 at 2:16 PM Prithviraj Nandigrami <
prithviraj.nandigrami.gmail.com> wrote:
> Hi,
>
> I am trying to use the native contacts analysis script implemented in
> CPPTRAJ as follows:
>
> *Without specifying a reference*
>
> parm step3_input.strip.parm7
> trajin combined.nc
> nativecontacts name NC1 :1-67&!.H= \
> writecontacts native-contacts.dat \
> resout resout.dat \
> distance 4.0 \
> 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
>
> *By specifying a reference*
>
> parm step3_input.strip.parm7
> trajin combined.nc
> reference ../step3_input.pdb
> nativecontacts name NC1 :1-67&!.H= \
> byresidue out nc.all.res.dat mindist maxdist \
> distance 3.0 reference map mapout resmap.gnu \
> contactpdb native-contacts.pdb \
> series seriesout native.dat
> run
>
>
> My question is: what do the columns in lifetime.dat, native.gnu,
> nonnative.gnu represent? I understand the residue indices in these files
> but do not understand the fractional values reported. Here is an example
> for native.gnu:
>
> 1.000 1.000 0.0000
> 1.000 2.000 16.6333
> 1.000 3.000 0.0000
> 1.000 4.000 0.0000
> 1.000 5.000 0.0000
> 1.000 6.000 0.0000
> 1.000 7.000 0.0000
> 1.000 8.000 0.0000
> 1.000 9.000 0.0000
> 1.000 10.000 0.0000
>
> and for nonnative.gnu:
>
> 1.000 1.000 0.0000
> 1.000 2.000 8.8826
> 1.000 3.000 0.9303
> 1.000 4.000 0.1229
> 1.000 5.000 0.0129
> 1.000 6.000 0.0060
> 1.000 7.000 0.0102
> 1.000 8.000 0.0004
> 1.000 9.000 0.0029
> 1.000 10.000 0.0012
> 1.000 11.000 0.0053
> 1.000 12.000 0.0024
> 1.000 13.000 0.0787
>
>
> What does the third column represent in these files?
>
> Thank you for your help and guidance!
> P.N.
>
>
>
>
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Received on Thu Jan 12 2023 - 15:30:02 PST
