Hi AMBER users,
When I use the ptraj command contacts I tend to see consistent "double
printing" of the number of contacts for the last residue.
Here is my input file below:
trajin ci2.pdb
contacts first byresidue out contacts.dat distance 5.0 .CA
matrix dist .CA out alldistmat.dat
And here is the output contacts.dat
#time residue 0 residue 1 residue 2 residue 3 residue 4
residue 5 residue 6 residue 7 residue 8 residue 9 residue
10 residue 11 residue 12 residue 13 residue 14 residue 15
residue 16 residue 17 residue 18 residue 19 residue 20
residue 21 residue 22 residue 23 residue 24 residue 25
residue 26 residue 27 residue 28 residue 29 residue 30
residue 31 residue 32 residue 33 residue 34 residue 35
residue 36 residue 37 residue 38 residue 39 residue 40
residue 41 residue 42 residue 43 residue 44 residue 45
residue 46 residue 47 residue 48 residue 49 residue 50
residue 51 residue 52 residue 53 residue 54 residue 55
residue 56 residue 57 residue 58 residue 59 residue 60
residue 61 residue 62 residue 63
1.00 1 2 2 3 2 3 2 2 2 3 2 3
2 2 2 2 2 2 2 2 4 2 2 3 3 2 2
3 3 3 3 2 3 3 2 2 2 2 2 2 2 3
3 2 2 3 4 3 3 3 4 2 2 2 2 3 4
2 2 3 2 3 3 33
Note how the number of contacts for the last residue is listed as 33. In VMD
I isolated the CA atoms within 5.0 angstroms of the last residue's CA atom
and only saw three contacts. And upon inspecting the distance matrix, here
is the distance data for the last residue:
12.928 12.265 8.677 9.855 12.599 14.701 17.610 16.475 17.055 20.034 19.859
20.278 17.722 20.026 20.068 16.336 15.633 18.481 17.019 13.459 15.136 17.460
14.882 12.699 15.291 13.662 10.507 10.032 10.413 10.872 13.119 13.805 16.447
15.534 16.117 14.857 14.098 10.865 10.371 8.721 7.554 *4.788 4.629*
5.402 7.218 5.439 6.066 7.482 10.887 12.699 16.370 19.713 22.957 23.937
20.878 19.649 16.274 16.533 13.644 11.941 9.323 6.327 *3.810 * 0.000
Note how only three residue pairs above are within 5A of one another: 4.788
4.629 3.810
Consistent with what I saw upon my inspection in VMD: 3 "contacts" within 5A
and at these same distances.
Upon adjusting the cutoff for the contacts command I obtained values like
11, 22, 1414 etc. and checking in VMD it was always just a double printing
of the true number of contacts. I saw the same double printing for the
output when using the contacts command on an MD trajectory vs. just a single
PDB file. I searched the listserv and couldn't really find anything
detailing this bug. Is there some way to fix this without writing a separate
script for processing these dat files?
Thank you for your help!!
-Liz W.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 11 2011 - 12:30:04 PST
