Hi,
No such change was made and I'm not able to reproduce your behavior.
Long explanation follows below but if it's at all possible could you
send me off-list some files I can use to reproduce the behavior?
I ran a quick test where I specified a reference that contained a
contact I knew would not be in the trajectory. Initially I get 23
contacts:
```
Setup 23 native contacts:
Atom ':
1.CA' to ':
2.CA'
Atom ':1.CA' to ':
3.CA'
Atom ':2.CA' to ':3.CA'
Atom ':
2.CA' to ':
4.CA'
Atom ':
3.CA' to ':
4.CA'
Atom ':3.CA' to ':5.CA'
Atom ':4.CA' to ':5.CA'
Atom ':
4.CA' to ':
6.CA'
Atom ':5.CA' to ':
6.CA'
Atom ':5.CA' to ':7.CA'
Atom ':
6.CA' to ':
7.CA'
Atom ':
6.CA' to ':
8.CA'
Atom ':6.CA' to ':9.CA'
Atom ':
7.CA' to ':
8.CA'
Atom ':
7.CA' to ':
9.CA'
Atom ':8.CA' to ':
9.CA'
Atom ':8.CA' to ':10.CA'
Atom ':
8.CA' to ':
11.CA'
Atom ':9.CA' to ':
10.CA'
Atom ':9.CA' to ':11.CA'
Atom ':
10.CA' to ':
11.CA'
Atom ':
10.CA' to ':
12.CA'
Atom ':11.CA' to ':
12.CA'
```
When the run completes I see that indeed, one of the native contacts
as defined by the reference is never present.
```
ACTION OUTPUT:
CONTACTS: TZ2
# Contact Nframes Frac. Avg Stdev
1 :3.CA_:4.CA 100 1 3.81 0.0452
2 :10.CA_:11.CA 100 1 3.81 0.0425
3 :9.CA_:10.CA 100 1 3.81 0.0421
4 :6.CA_:
7.CA 100 1 3.81 0.0416
5 :
11.CA_:
12.CA 100 1 3.81 0.0434
6 :
5.CA_:
6.CA 100 1 3.81 0.0353
7 :8.CA_:9.CA 100 1 3.81 0.042
8 :7.CA_:8.CA 100 1 3.81 0.0345
9 :4.CA_:5.CA 100 1 3.82 0.0372
10 :2.CA_:3.CA 100 1 3.82 0.0381
11 :
1.CA_:
2.CA 100 1 3.82 0.0383
12 :
3.CA_:
5.CA 100 1 5.67 0.352
13 :1.CA_:3.CA 100 1 5.74 0.4
14 :2.CA_:4.CA 100 1 6.26 0.33
15 :5.CA_:7.CA 100 1 6.35 0.309
16 :9.CA_:11.CA 100 1 6.37 0.275
17 :4.CA_:
6.CA 98 0.98 6.34 0.378
18 :
10.CA_:
12.CA 97 0.97 6.38 0.268
19 :
8.CA_:
10.CA 96 0.96 6.46 0.285
20 :7.CA_:9.CA 95 0.95 6.32 0.387
21 :6.CA_:8.CA 74 0.74 6.5 0.314
22 :6.CA_:9.CA 5 0.05 6.55 0.322
23 :8.CA_:
11.CA 0 0 0 0
```
The 'resout' output shows the contact that was never present, even
though the total fraction is zero:
```
#Res1 #Res2 TotalFrac Contacts
1 2 1 1
1 3 1 1
2 3 1 1
2 4 1 1
3 4 1 1
3 5 1 1
4 5 1 1
5 6 1 1
5 7 1 1
6 7 1 1
7 8 1 1
8 9 1 1
9 10 1 1
9 11 1 1
10 11 1 1
11 12 1 1
4 6 0.98 1
10 12 0.97 1
8 10 0.96 1
7 9 0.95 1
6 8 0.74 1
6 9 0.05 1
8 11 0 1
```
This was run with cpptraj v16.00. Let me know if you have any questions.
-Dan
On Fri, May 27, 2016 at 3:25 AM, Eiros Zamora, Juan
<j.eiros-zamora14.imperial.ac.uk> wrote:
> Dear Amberists,
>
> I’ve noticed that after the upgrade to AmberTools16 the ‘resout' flag of the nativecontacts function in cpptraj does not print anymore the residue pairs if the ‘TotalFrac’ value is 0.
>
> While I appreciate that this might be done to save memory/space, it interferes with the scripts that I have to plot the results from this analysis. Is there anyway to revert back to the ‘old’ print mode? I’ve looked in the new manual but I’ve not found any mention to this change.
>
> Best,
>
> [Imperial College London] <http://www.icb-cdt.co.uk/>
>
>
> Juan Eiros Zamora / PhD Student
> je714.ic.ac.uk<mailto:je714.ic.ac.uk> / +44 (0) 7783018326
>
> Imperial College London
> Imperial College Road SW7 2AZ | UK
> http://www.icb-cdt.co.uk/
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri May 27 2016 - 08:00:03 PDT
