Dear Amber users and developers,
I’ve successfully updated Amber package by the command:
$AMBERHOME/update_amber —upgrade
Followed by:
cd $AMBERHOME
./configure -macAccelerate clang
make install
make test
From which I got:
Finished serial test suite for Amber 17 at Wed May 23 15:36:37 CEST 2018.
150 file comparisons passed
0 file comparisons failed
0 tests experienced errors
Test log file saved as /Users/administrateur/amber16/logs/test_amber_serial/2018-05-23_15-29-32.log
No test diffs to save!
Summary of AmberTools serial tests:
1959 file comparisons passed
20 file comparisons failed
4 tests experienced errors
Test log file saved as /Users/administrateur/amber16/logs/test_at_serial/2018-05-23_13-53-59.log
Test diffs file saved as /Users/administrateur/amber16/logs/test_at_serial/2018-05-23_13-53-59.diff
Now, I do not get the previous error message when trying to compute the nativecontacts command, yet I get empty files.. (attached). Could you please point me out a working example so I adapt my input file? I would highly appreciate some guidance in this matter as, despite taking as a reference the input file given in the manual, I’m not understanding how to use this command.
Thanking you in advance,
Sincerely,
Ruth
> On 23 May 2018, at 10:43, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
>
> Dear Andy,
>
> I’m using CPPTRAJ: Trajectory Analysis. V16.16
> I’ll upgrade to Ambertools17 then and try again.
>
> Thanks for your help,
>
> Sincerely,
>
> Ruth
>
>> On 23 May 2018, at 10:15, Andreas Tosstorff <andreas.tosstorff.cup.uni-muenchen.de> wrote:
>>
>> Hi Ruth,
>>
>> Which cpptraj version are you using? I think nonnative is only supported
>> in more recent versions. Try updating cpptraj/ambertools.
>>
>> Best,
>> Andy
>>
>> On 05/23/2018 10:09 AM, Ruth Helena Tichauer wrote:
>>> Dear Daniel,
>>>
>>> Thank you for your answer.
>>>
>>> I’ve changed my input file to the following:
>>>
>>> #Load topology and trajectories
>>> parm ../../native2.parm
>>> trajin ../../../../2/Neutralized/nat2_md-qm.nc
>>> trajin ../../nat-ew2-0_mdqm.nc
>>> trajin ../../nat-ew2-0_mdqm1.nc
>>> trajin ../../nat-ew2-0_mdqm2.nc
>>> trajin ../../nat-ew2-0_mdqm3.nc
>>> trajin ../../nat-ew2-0_mdqm4.nc
>>> trajin ../../nat-ew2-0_mdqm5.nc
>>> trajin ../../nat-ew2-0_mdqm6.nc
>>> trajin ../../nat-ew2-0_mdqm7.nc
>>> trajin ../../nat-ew2-0_mdqm8.nc
>>> trajin ../../nat-ew2-0_mdqm9.nc
>>> trajin ../../nat-ew2-0_mdqm10.nc
>>> trajin ../../nat-ew2-0_mdqm11.nc
>>> trajin ../../nat-ew2-0_mdqm12.nc
>>> trajin ../../nat-ew2-0_mdqm13.nc
>>> trajin ../../nat-ew2-0_mdqm14.nc
>>> trajin ../../nat-ew2-0_mdqm15.nc
>>> trajin ../../nat-ew2-0_mdqm16.nc
>>> trajin ../../nat-ew2-0_mdqm17.nc
>>> trajin ../../nat-ew2-0_mdqm18.nc
>>> trajin ../../nat-ew2-0_mdqm19.nc
>>> reference ../../../../2/Neutralized/nat2_md-qm_0.pdb
>>>
>>> #Native contacts analysis
>>> nativecontacts name nat2-0_NC :179&!.CA,C,O,N,H \
>>> byresidue resoffset 4 out nat2-0_NC-179.nb \
>>> noimage distance 8.0 reference \
>>> writecontacts nat2-0_NC-179.out \
>>> resout nat2-0_NC-179.resout \
>>> series seriesout nat2-0_NC-179.nc_vs_t \
>>> savenonnative seriesnnout nat2-0_NN-179.nn_vs_t \
>>> map mapout nat2-0_NC-179 \
>>>
>>> But I get the following error message:
>>>
>>> Error: [nativecontacts] Not all arguments handled: [ savenonnative seriesnnout nat2-0_NN-179.nn_vs_t ]
>>> 1 errors encountered reading input.
>>> TIME: Total execution time: 1.9272 seconds.
>>> Error: Error(s) occurred during execution.
>>>
>>> I’ve carefully read the manual, several times, but yet I don’t manage to write a working input file.. As well, I do not understand for what the option “name” is used. As you can see, I’ve included it in my input file because it is in the example given in the manual but honestly, I don’t understand its behaviour.
>>>
>>> Moreover, I want to get both native and nonnative contacts but with my original input file, I don’t even get native contacts despite that the visualisation of the reference structure showed residues within the chosen cutoff interacting with residue 179 defined in the mask.
>>>
>>> Please help me build a correct input file.
>>>
>>> Thanking you in advance,
>>>
>>> Ruth
>>>
>>>> On 22 May 2018, at 15:33, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>>
>>>> Hi,
>>>>
>>>> On Tue, May 22, 2018 at 9:25 AM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
>>>>> Dear Amber developers,
>>>>>
>>>>> I’ve been trying to use the nativecontacts command without success so I’m posting again the question I’d asked few days ago.
>>>> Andreas suggested that you may need the non-native option
>>>> ('savenonnative' etc) of the native contacts command, but you don't
>>>> appear to have tried it. Please read the Amber manual entry for the
>>>> 'nativecontacts' command for more details.
>>>>
>>>>> Prior, I used the cat linux command to append several trajectories into a single one, but instead of getting a trajectory containing around 5000 frames I get one with 250 frames only, which corresponds to a single portion of my simulation.. This is the exact command in case you could help me spot a mistake:
>>>> Yikes - don't do this! In most cases the 'cat' command should not be
>>>> used to string together formatted files, and certainly not binary ones
>>>> like the NetCDF format. The correct way to concatenate trajectories is
>>>> to read them into a trajectory processing program (like cpptraj) and
>>>> output them, e.g.
>>>>
>>>> trajin traj1.nc
>>>> trajin traj2.nc
>>>> trajin traj3.nc
>>>> trajout combined.nc
>>>>
>>>> Hope this helps,
>>>>
>>>> -Dan
>>>>
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>>>>
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>>
>> --
>>
>>
>> --
>> M.Sc. Andreas Tosstorff
>> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
>> Department Pharmazie
>> LMU München
>> Butenandtstr. 5-13 ( Haus B)
>> 81377 München
>> Germany
>> Tel.: +49 89 2180 77059
>>
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>>
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Received on Wed May 23 2018 - 08:30:02 PDT
