One question regarding analysis of the stripped trajectories:
I've tried to make the same analysis for the dcd stripped from the solvent using
parm /data2/Gleb/TEST/claire+7d4+md/water_analysis/md1_wat_long/top_all/7D4-sauv.top
trajin /data2/Gleb/TEST/claire+7d4+md/water_analysis/md1_wat_long/trr_all/7d4_sauv.dcd
250 last 50
autoimage
strip !(:2-290) outprefix strip
trajout
Then loading both stripped files for dihedral analysis
parm /data2/Gleb/TEST/claire+7d4+md/water_analysis/md1_wat_long/tops_MD2/stripped_7D4-sauv.top
trajin /data2/Gleb/TEST/claire+7d4+md/water_analysis/md1_wat_long/trr_MD2/7d4_APO_MD2.dcd
250 last 50
autoimage
dihedral Dihedral_7d4_APO_MD2 :235.CA :235.CB :235.CG :235.CD1 out
/data2/Gleb/TEST/claire+7d4+md/water_analysis/md1_wat_long/resultsMD2/strip_7d4_APO_MD2.xm
I obtained error:
g/tops_MD2/7d4_androste_MD2.top' (1 actions):
0: [dihedral Dihedral_7d4_androste_MD2 :235.CA :235.CB :235.CG
:235.CD1 out /data2/Gleb/TEST/claire+7d4+md/water_analysis/md1_wat_long/xz/strip_7d4_androste_MD2.xm]
[:235.CA](1) [:235.CB](0) [:235.CG](0) [:235.CD1](0)
Warning: dihedral: One or more masks have no atoms.
Warning: Setup failed for [dihedral Dihedral_7d4_androste_MD2 :235.CA
:235.CB :235.CG :235.CD1 out
/data2/Gleb/TEST/claire+7d4+md/water_analysis/md1_wat_long/xz/strip_7d4_androste_MD2.xm]:
Skipping
are there some special rules to work with such dcd files ?
James
2015-03-27 17:33 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
> On Fri, Mar 27, 2015 at 10:28 AM, James Starlight
> <jmsstarlight.gmail.com> wrote:
>> use :
>> multidihedral chi_toogle chip resrange 1-10 out dihedral.agr
>>
>> or it should to provide precise atom names like
>>
>> multidihedral chi_toogle :.CA:.CB:.CG:.CD1 resrange 1-10 out dihedral.agr
>
> The former should work. As always, you should run this on a small
> subset of your data (say no more than 100 frames) before trying
> production, and examine your output carefully for any 'Warning:' or
> 'Error:' messages. Make sure you get all of the dihedrals you expect.
>
> -Dan
>
>>
>> James
>>
>> 2015-03-27 16:39 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
>>> Hi,
>>>
>>> You'll need to use the 'dihedral' or 'multidihedral' commands to
>>> generate the dihedral data. If using 'multidihedral' it's important to
>>> issue a 'run' command before any analysis. Then use the 'hist', 'kde
>>> or 'multihist' analysis commands to generate histograms (either same
>>> step or subsequent step). In addition you can use the 'stat' analysis
>>> command to obtain more detailed info on the dihedrals. For example, to
>>> look at all phi distributions for residues 1-10:
>>>
>>> parm myparm.parm7
>>> trajin mytraj.nc
>>> multidihedral MyDihedral phi resrange 1-10 out dihedral.agr
>>> run
>>> multihist MyDihedral[*] out hist.dihedral.agr normint min -180 max 180 step 1
>>> stat all out stat.dihedral.dat
>>>
>>> Hope this helps,
>>>
>>> -Dan
>>>
>>> On Fri, Mar 27, 2015 at 9:13 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>>>> Dear Amber users!
>>>>
>>>> I need to analyze several md trajectories of the receptor-ligand
>>>> complexes to obtain some structural information on level of receptor's
>>>> individual residues. For each of the trajectory I need to calculate
>>>> distributions of dihedral angles within specified receptor's residues
>>>> and obtain the information in histogram form to compare such outputs
>>>> and to see how the presence of different ligands alter its equilibrium
>>>> dynamics. I'll be expecially thankful for example of cpptraj commands
>>>> sequence for such kind of the analysis as well as its additional tools
>>>> which could produce relevant information in my task.
>>>>
>>>> Thanks alot!
>>>>
>>>> James
>>>>
>>>> _______________________________________________
>>>> 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)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 30 2015 - 04:00:04 PDT
