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.
I’ve used the following input file:
#Load topology and trajectories
parm ../../native2.parm
trajin ../../nat_2-ew19.nc
reference ../../../../2/Neutralized/nat2_md-qm_0.pdb
#Native contacts analysis
nativecontacts name nat2-0_NC noimage distance 8.0 :179&
!.CA,C,O,N,H \
byresidue resoffset 4 out nat2-0_NC-179.nb \
writecontacts nat2-0_NC-179.out \
resout nat2-0_NC-179.resout \
series seriesout nat2-0_NC-179.nc_vs_t \
map mapout nat2-0_NC-179 \
And I’ve got the following messages when executing.
CPPTRAJ: Trajectory Analysis. V16.16
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 05/22/18 15:00:43
| Available memory: 133.280 MB
INPUT: Reading input from 'nat2-0_NC.in'
[parm ../../native2.parm]
Reading '../../native2.parm' as Amber Topology
[trajin ../../nat_2-ew19.nc]
Reading '../../nat_2-ew19.nc' as Amber NetCDF
[reference ../../../../2/Neutralized/nat2_md-qm_0.pdb]
Reading '../../../../2/Neutralized/nat2_md-qm_0.pdb' as PDB
Read CRYST1 info from PDB: a=62.134 b=62.134 c=62.134 alpha=109.47 beta=109.47 gamma=109.47
Warning: Low precision truncated octahedron angles detected (109.47 vs 109.471).
Warning: If desired, the 'box' command can be used during processing
Warning: to set higher-precision angles.
Read CRYST1 info from PDB: a=62.134 b=62.134 c=62.134 alpha=109.47 beta=109.47 gamma=109.47
Setting active reference for distance-based masks: 'nat2_md-qm_0.pdb'
[nativecontacts name nat2-0_NC noimage distance 8.0 :179&
!.CA,C,O,N,H byresidue resoffset 4 out nat2-0_NC-179.nb writecontacts nat2-0_NC-179.out resout nat2-0_NC-179.resout series seriesout nat2-0_NC-179.nc_vs_t map mapout nat2-0_NC-179 ]
Warning: No reference structure specified. Defaulting to first.
NATIVECONTACTS: Mask1=':179&!.CA,C,O,N,H', contacts set up based on first frame.
Contacts will be ignored for residues spaced < 5 apart.
Map will be printed by residue.
Distance cutoff is 8 Angstroms, imaging is off.
Mask selection will not include solvent.
Data set name: nat2-0_NC
Output to 'nat2-0_NC-179.nb'
Contact stats will be written to 'nat2-0_NC-179.out'
Contact res pairs will be written to 'nat2-0_NC-179.resout'
Native contacts map will be saved as set 'nat2-0_NC[nativemap]'
Non-native contacts map will be saved as set 'nat2-0_NC[nonnatmap]'
Native map output to 'native.nat2-0_NC-179'
Native map output to 'nonnative.nat2-0_NC-179'
Saving native contact time series nat2-0_NC[NC].
Writing native contact time series to nat2-0_NC-179.nc_vs_t
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: native2.parm, 15564 atoms, 4403 res, box: Trunc. Oct., 4222 mol, 4204 solvent
INPUT TRAJECTORIES (1 total):
0: 'nat_2-ew19.nc' is a NetCDF AMBER trajectory, Parm native2.parm (Trunc. Oct. box) (reading 250 of 250)
Coordinate processing will occur on 250 frames.
REFERENCE FRAMES (1 total):
0: nat2_md-qm_0.pdb:1
Active reference frame for distance-based masks is 'nat2_md-qm_0.pdb:1'
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'native2.parm' (1 actions):
0: [nativecontacts name nat2-0_NC noimage distance 8.0 :179&
!.CA,C,O,N,H byresidue resoffset 4 out nat2-0_NC-179.nb writecontacts nat2-0_NC-179.out resout nat2-0_NC-179.resout series seriesout nat2-0_NC-179.nc_vs_t map mapout nat2-0_NC-179 ]
Mask [:179&!.CA,C,O,N,H] corresponds to 19 atoms.
19 potential contact sites for ':179&!.CA,C,O,N,H'
Imaging disabled.
----- nat_2-ew19.nc (1-250, 1) -----
Using first frame to determine native contacts.
Mask [:179&
!.CA,C,O,N,H] corresponds to 19 atoms.
Setup 0 native contacts:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 250 frames and processed 250 frames.
TIME: Avg. throughput= 280.6192 frames / second.
ACTION OUTPUT:
CONTACTS: nat2-0_NC: Writing native contacts to file 'nat2-0_NC-179.out'
DATASETS (4 total):
nat2-0_NC[native] "nat2-0_NC[native]" (integer), size is 250
nat2-0_NC[nonnative] "nat2-0_NC[nonnative]" (integer), size is 250
nat2-0_NC[nativemap] "nat2-0_NC[nativemap]" (double matrix), size is 1
nat2-0_NC[nonnatmap] "nat2-0_NC[nonnatmap]" (double matrix), size is 1
DATAFILES (6 total):
nat2-0_NC-179.nb (Standard Data File): nat2-0_NC[native] nat2-0_NC[nonnative]
nat2-0_NC-179.nc_vs_t (Standard Data File):
native.nat2-0_NC-179 (Standard Data File): nat2-0_NC[nativemap]
nonnative.nat2-0_NC-179 (Standard Data File): nat2-0_NC[nonnatmap]
nat2-0_NC-179.out (Native Contacts)
nat2-0_NC-179.resout (Contact Res Pairs)
Warning: File 'nat2-0_NC-179.nc_vs_t' has no sets containing data.
RUN TIMING:
TIME: Init : 0.0001 s ( 0.01%)
TIME: Trajectory Process : 0.8909 s ( 95.14%)
TIME: Action Post : 0.0296 s ( 3.16%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0158 s ( 1.69%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 0.9364 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1.3700 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
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:
cat ../../2/Neutralized/nat2_md-qm.nc nat-ew2-0_mdqm.nc nat-ew2-0_mdqm1.nc nat-ew2-0_mdqm2.nc nat-ew2-0_mdqm3.nc nat-ew2-0_mdqm4.nc nat-ew2-0_mdqm5.nc nat-ew2-0_mdqm6.nc nat-ew2-0_mdqm7.nc nat-ew2-0_mdqm8.nc nat-ew2-0_mdqm9.nc nat-ew2-0_mdqm10.nc nat-ew2-0_mdqm11.nc nat-ew2-0_mdqm12.nc nat-ew2-0_mdqm13.nc nat-ew2-0_mdqm14.nc nat-ew2-0_mdqm15.nc nat-ew2-0_mdqm16.nc nat-ew2-0_mdqm17.nc nat-ew2-0_mdqm18.nc nat-ew2-0_mdqm19.nc > nat_2-ew19.nc
When I visualise the reference structure, several atoms from a ligand which is numbered 169, are within the cutoff distance I have chosen, yet as you can see, the files I get are empty for both native and nonnative contacts (see attachments).. I don’t know wether:
-How to change my input file in order to get the by residue native contacts present in the initial structure, given as a reference, and then show that these native contacts are lost and others are formed (non native contacts become native contacts).
-I’m misunderstanding the functionality of this command.
Please help me correct my input file to obtain the desired results (if possible).
Thanks in advance,
Sincerely,
Ruth
> On 6 May 2018, at 18:26, Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:
>
> Hey Ruth,
>
> Yes, you can include the reference as anything you mention, sorry I forgot to mention it in my previous email. if you don't want to re-image your coordinates, you can avoid this.
>
> Just add the reference flag in the contact command after having defined what the reference structure is.
>
> Also refer to page 600 (http://ambermd.org/doc12/Amber16.pdf) for more info. about the same.
>
> I hope this helps,
>
> Regards
>
> Sowmya
>
> ________________________________
> From: Ruth Helena Tichauer <rhtichau.laas.fr>
> Sent: Sunday, May 6, 2018 5:58:09 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] nativecontacts command in CPPTRAJ
>
> Dear Sowmya,
>
> Thank you for your suggestion.
>
> However, I didn’t “wrap” the coordinates so, if I understand correct, I don’t need to do autoimage, right? Also, I wish to take as a reference the structure I load as a reference rather than the first frame.. Could modifications include these features?
>
> Thank you,
>
> Ruth
>
>
>> On 6 May 2018, at 17:13, Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:
>>
>> Hey Ruth,
>>
>> You may want to try this, this works fine for me:
>>
>>
>> parm file.parm7
>>
>> trajin pH.nc
>>
>> autoimage
>> strip :WAT #optional
>> reference min.rst7
>> nativecontacts :179&!.CA,C,O,N,H writecontacts nativecontacts.dat resout res noimage distance 8.0 out contacts.out first resoffset 4 contactpdb contacts.pdb byresidue map mapout gnu series seriesout nativeseries.dat
>>
>> Regards
>> Sowmya
>>
>>
>> ________________________________
>> From: Ruth Helena Tichauer <rhtichau.laas.fr>
>> Sent: Sunday, May 6, 2018 12:31:06 PM
>> To: AMBER Mailing List
>> Subject: [AMBER] nativecontacts command in CPPTRAJ
>>
>> Dear Amber users and developers,
>>
>> I’ve run QM/MM simulations of a protein with its ligand.
>>
>> While visualising the obtained trajectories, I’ve noticed that a given residue (179) engages in different interactions in the initial structure and during the production phase. To depict this structural rearrangements, I wanted to use the nativecontacts command from CPPTRAJ in a manner that it would calculate the by residue native contacts present in the initial structure, given as a reference, and then show that these native contacts are lost and others are formed (non native contacts become native contacts) using the following input file:
>>
>> #Load topology and trajectories
>> parm ../native2.parm
>> trajin ../nat2-0_0_19.nc
>> reference ../../../2/Neutralized/nat2_md-qm_0.pdb parm ../native2.parm
>>
>> #Native contacts analysis
>> nativecontacts :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 \
>> map mapout nat2-0_NC-179 \
>>
>> Nevertheless I get empty files.. As it is the first time I’m using this command, I suspect there are some errors in it, please help me correct it in order to get the information I wish (native contacts vs time, non native contacts vs time, strength of contacts made, lasting native contacts..).
>>
>> Thank you in advance,
>>
>> Ruth
>> _______________________________________________
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>>
>
>
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Received on Tue May 22 2018 - 06:30:03 PDT
