Dear all,
i want to calculate the native contacts in my protein by using ptraj
contacts command. i am little confused when looking in the output. for
example i calculate the contact for mask 1-5 residue and the output was
like this
#time residue 0 residue 1 residue 2 residue 3 residue 4
1.00 495 778 972 689 69226
2.00 454 775 885 673 64727
3.00 475 758 976 683 70428
4.00 459 767 952 701 70526
5.00 479 789 932 700 67426
*why is the last column showing very big number which is definitely not
possible in case of my protein?*
when i run for the residue 1 to 6, the result was
#time residue 0 residue 1 residue 2 residue 3 residue 4
residue 5
1.00 495 778 981 872 867 88931
2.00 454 775 893 869 829 91231
3.00 475 758 988 859 893 90129
4.00 459 767 957 855 900 88428
5.00 479 790 939 903 870 93730
This time the residue 4 looks reasonable but again last resid have large
number. and *Why there is inconsistancies in the number of native contacts
even for residue 3 although i submitted same snapshots with same cutoff?
Please clarify me.*
Thank you in advance
Regards,
Rajeswari A
Computational biophysics lab,
IIT Madras
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Received on Sat Jan 21 2012 - 04:30:04 PST
