Hi,
Glad to hear you solved it. Presumably the issue was that you didn't
initially take into account that residues are renumbered once you
strip? For example, in a system with 3 residues:
ASP1 ALA2 ARG3
If you execute 'strip :2' (strip residue 2) then ARG3 is now the second residue:
ASP1 ARG2
Was that the issue?
-Dan
On Mon, Mar 30, 2015 at 4:52 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> 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
--
-------------------------
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 Mon Mar 30 2015 - 07:30:09 PDT
