Hi,
Thanks for the files. The first thing that pops out to me when I
compare your old output and new is this:
OLD:
```
Mask [:1-89] corresponds to 1363 atoms.
Mask [:249-289] corresponds to 642 atoms.
Setup 875046 native contacts:
```
NEW:
```
Mask [:1-89] corresponds to 1363 atoms.
Mask [:249-289] corresponds to 642 atoms.
Setup 5932 native contacts:
```
For your old output it sets up native contacts for every single atom
pair (1363 * 642), which seems highly unlikely to me. The new results
seem much more reasonable. A brief scan of the development logs
doesn't show any obvious changes to 'nativecontacts' that would affect
this. Could you send me off-list the average structures generated from
versions 15 and 16 of cpptraj along with the corresponding topology
(since this is what you are using to determine your native contacts)?
Thanks.
-Dan
On Fri, May 27, 2016 at 8:54 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
--
-------------------------
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 - 13:30:03 PDT
