Hi,
I can confirm that this is a bug. What is happening is that during the
'strip' command the reference coordinates are not being copied, so
when you get to the 'cluster' command that reference for the
distance-based mask is no longer available. There are two workarounds.
The first is you can save a stripped coordinate trajectory and
corresponding topology and work from there. I actually recommend this
because it is likely that most analysis you do will not require water,
and processing the stripped trajectory is much faster (although save
the original trajectory unless you are very VERY sure you don't need
it!):
parm PknGHAdeH_ion_wt.prmtop
trajin ../../PknGAde_md_reimage20ns.mdcrd
strip :WAT outprefix PknGAde_nowat
trajout nowat.PknGAde_md_reimage20ns.nc netcdf
You can then work from your stripped topology and coordinates,
PknGAde_nowat.PknGHAdeH_ion_wt.prmtop and
nowat.PknGAde_md_reimage20ns.nc, with no issues.
The second is to just work from the solvated trajectory. If you do
that you will probably have to add '&!:WAT' to your atom masks to
exclude water. You will also need more memory to store the
coordinates.
In the meantime I will be working on a bugfix that should be released
soon. Hope this helps for now,
-Dan
On Wed, Aug 13, 2014 at 8:25 AM, Valentina Romano
<valentina.romano.unibas.ch> wrote:
> Yes, sorry for the mistake.
>
> Input:
> trajin ../../PknGAde_md_reimage20ns.mdcrd
> strip :WAT outprefix PknGAde_nowat
> reference ../../../PknGAde_md_sequel01.rst
> cluster out cnumvtime.dat summary PknGAde20nsClusteringSummary.txt repout PknGAde_20ns.pdb repfmt pdb clusterout PknGAde_20ns.nc clusterfmt averagelinkage clusters 5 rms sieve 10 :247<:5.0
>
> output:
> CPPTRAJ: Trajectory Analysis. V13.22
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> AmberParm Title: [default_name]
> Radius Set: modified Bondi radii (mbondi)
> INPUT: Reading Input from file cluster.in
> [trajin ../../PknGAde_md_reimage20ns.mdcrd]
> [PknGAde_md_reimage20ns.mdcrd] contains 20000 frames.
> [strip :WAT outprefix PknGAde_nowat]
> STRIP: Stripping atoms in mask [:WAT]
> Stripped topology will be output with prefix PknGAde_nowat
> [reference ../../../PknGAde_md_sequel01.rst]
> [PknGAde_md_sequel01.rst] contains 1 frames.
> [PknGAde_md_sequel01.rst] is an AMBER restart file with velocity info, Parm PknGHAdeH_ion_wt.prmtop (Orthogonal box) (reading 1 of 1)
> [cluster out cnumvtime.dat summary PknGAde20nsClusteringSummary.txt repout PknGAde_20ns.pdb repfmt pdb clusterout PknGAde_20ns.nc clusterfmt averagelinkage clusters 5 rms sieve 10 :247<:5.0]
> Warning: No clustering algorithm specified; defaulting to 'hieragglo'
> CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:247<:5.0]) best fit
> Hierarchical Agglomerative: 5 clusters, average-linkage.
> Initial clustering sieve value is 10 frames.
> Cluster # vs time will be written to cnumvtime.dat
> Summary of cluster results will be written to PknGAde20nsClusteringSummary.txt
> Cluster trajectories will be written to PknGAde_20ns.nc, format Amber Trajectory
> Cluster representatives will be written to separate trajectories,
> prefix (PknGAde_20ns.pdb), format PDB
> Warning: One or more analyses requested creation of default COORDS DataSet.
> CREATECRD: Saving coordinates from Top PknGHAdeH_ion_wt.prmtop to "_DEFAULTCRD_"
>
> PARAMETER FILES:
> 0: PknGHAdeH_ion_wt.prmtop, 28424 atoms, 8443 res, box: Orthogonal, 8198 mol, 8190 solvent, 20000 frames
>
> INPUT TRAJECTORIES:
> 0: [PknGAde_md_reimage20ns.mdcrd] is an AMBER trajectory, Parm PknGHAdeH_ion_wt.prmtop (Orthogonal box) (reading 20000 of 20000)
> Coordinate processing will occur on 20000 frames.
>
> REFERENCE COORDS:
> The following 1 frames have been defined:
> 0: PknGAde_md_sequel01.rst frame 1
> Active reference frame for masks is 0
>
> OUTPUT TRAJECTORIES:
> No files.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM [PknGHAdeH_ion_wt.prmtop] (2 actions):
> 0: [strip :WAT outprefix PknGAde_nowat]
> Stripping 24570 atoms.
> Topology PknGHAdeH_ion_wt.prmtop contains 3854 atoms.
> 253 residues.
> 3889 bonds.
> 8 molecules.
> Box: Orthogonal
> Writing out amber topology file PknGHAdeH_ion_wt.prmtop to PknGAde_nowat.PknGHAdeH_ion_wt.prmtop
> 1: [createcrd _DEFAULTCRD_]
> ----- [PknGAde_md_reimage20ns.mdcrd] (1-20000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 20000 frames and processed 20000 frames.
>
> ACTION OUTPUT:
>
> DATASETS:
> 2 data sets:
> _DEFAULTCRD_ "_DEFAULTCRD_" (coords), size is 20000 PknGHAdeH_ion_wt.prmtop, 3854 atoms, 253 res, box: Orthogonal, 8 mol
> Cnum_00001 "Cnum_00001" (integer), size is 0
>
> ANALYSIS: Performing 1 analyses:
> 0: [cluster out cnumvtime.dat summary PknGAde20nsClusteringSummary.txt repout PknGAde_20ns.pdb repfmt pdb clusterout PknGAde_20ns.nc clusterfmt averagelinkage clusters 5 rms sieve 10 :247<:5.0]
> Starting clustering.
> Error: No reference set for [PknGHAdeH_ion_wt.prmtop], cannot select by distance.
> Calculating pair-wise distances.
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
> Starting Hierarchical Agglomerative Clustering:
> Progress: '+' = 200 iterations.
> 2000 initial clusters.
> 0 +++++++++
> Target # of clusters (5) met (5), clustering complete.
> Completed after 1994 iterations, 5 clusters.
> Restoring non-sieved frames.
> Cluster Init.: 0.00 seconds.
> Pairwise Calc.: 2.01 seconds.
> Clustering: 11.55 seconds.
> Cluster Post.: 103.86 seconds.
> Total: 117.42 seconds.
>
>
> DATASETS AFTER ANALYSIS:
> 2 data sets:
> _DEFAULTCRD_ "_DEFAULTCRD_" (coords), size is 20000 PknGHAdeH_ion_wt.prmtop, 3854 atoms, 253 res, box: Orthogonal, 8 mol
> Cnum_00001 "Cnum_00001" (integer), size is 20000
> DATAFILE OUTPUT:
> cnumvtime.dat: Cnum_00001
> cnumvtime.dat: Writing 20000 frames.
> --------------------------------------------------------------------------------
>
> Do you think the reference structure was taking into account or not?
>
> Thank you
> Vale
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
>
> ________________________________________
> From: Marc van der Kamp [marcvanderkamp.gmail.com]
> Sent: Wednesday, August 13, 2014 3:22 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Cluster results
>
> Hi,
> It doesn't look like the output file you copied in your email is related to
> the input. See in particular this section of the output:
> INPUT: Reading Input from file reimage.ptraj
> [trajin ../vSrcI338G-benzyl1731-md.mdcrd]
> [vSrcI338G-benzyl1731-md.mdcrd] contains 2000 frames.
> [trajout vSrcI338G-benzyl1731-md-reimage.mdcrd]
> [center :1-257]
> CENTER: To box center via center of geometry using atoms in mask :1-257
> [image familiar]
> IMAGE: By molecule to box center based on first atom position using
> atoms in mask *
> Triclinic On, familiar shape.
> [go]
>
> I don't think you pasted the input from reimage.ptraj, but you did paste
> the output related to this.
> --Marc
>
>
> On 13 August 2014 13:59, Valentina Romano <valentina.romano.unibas.ch>
> wrote:
>
>> Hi
>>
>> I used a reference structure in the clustering process.
>>
>> I used the following input file:
>>
>> trajin ../../PknGAde_md_reimage20ns.mdcrd
>> strip :WAT outprefix PknGAde_nowat
>> reference ../../../PknGAde_md_sequel01.rst
>> cluster out cnumvtime.dat summary PknGAde20nsClusteringSummary.txt repout
>> PknGAde_20ns.pdb repfmt pdb clusterout PknGAde_20ns.nc clusterfmt
>> averagelinkage clusters 5 rms sieve 10 :247<:5.0
>>
>> The output file was:
>> CPPTRAJ: Trajectory Analysis. V13.22
>> ___ ___ ___ ___
>> | \/ | \/ | \/ |
>> _|_/\_|_/\_|_/\_|_
>> AmberParm Title: [default_name]
>> Radius Set: H(N)-modified Bondi radii (mbondi2)
>> INPUT: Reading Input from file reimage.ptraj
>> [trajin ../vSrcI338G-benzyl1731-md.mdcrd]
>> [vSrcI338G-benzyl1731-md.mdcrd] contains 2000 frames.
>> [trajout vSrcI338G-benzyl1731-md-reimage.mdcrd]
>> [center :1-257]
>> CENTER: To box center via center of geometry using atoms in mask :1-257
>> [image familiar]
>> IMAGE: By molecule to box center based on first atom position using
>> atoms in mask *
>> Triclinic On, familiar shape.
>> [go]
>>
>> PARAMETER FILES:
>> 0: vSrcI338G-benzyl1731-solv.prmtop, 25380 atoms, 7353 res, box:
>> Orthogonal, 7098 mol, 7093 solvent, 2000 frames
>>
>> INPUT TRAJECTORIES:
>> 0: [vSrcI338G-benzyl1731-md.mdcrd] is an AMBER trajectory, Parm
>> vSrcI338G-benzyl1731-solv.prmtop (Orthogonal box) (reading 2000 of 2000)
>> Coordinate processing will occur on 2000 frames.
>>
>> REFERENCE COORDS:
>> No frames defined.
>>
>> OUTPUT TRAJECTORIES:
>> [vSrcI338G-benzyl1731-md-reimage.mdcrd] is an AMBER trajectory, Parm
>> vSrcI338G-benzyl1731-solv.prmtop: Writing 2000 frames (1-Last, 1)
>>
>> BEGIN TRAJECTORY PROCESSING:
>> .....................................................
>> ACTION SETUP FOR PARM [vSrcI338G-benzyl1731-solv.prmtop] (2 actions):
>> 0: [center :1-257]
>> Mask [:1-257] corresponds to 4098 atoms.
>> 1: [image familiar]
>> Number of molecules to be imaged is 7098 based on mask [*]
>> ----- [vSrcI338G-benzyl1731-md.mdcrd] (1-2000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> Read 2000 frames and processed 2000 frames.
>>
>> ACTION OUTPUT:
>>
>> DATASETS:
>> No data sets.
>>
>> --------------------------------------------------------------------------------
>>
>> To me, It looked like the the reference structure was not take into
>> account.
>> Can you help me to understand what was wrong in my input file?
>>
>> Thank you.
>> Best,
>> Valentina
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB
>> Swiss Institute of Bioinformatics
>> Klingelbergstrasse 61 | CH-4056 Basel |
>>
>> Phone: +41 61 267 15 80
>>
>>
>> ________________________________________
>> From: Daniel Roe [daniel.r.roe.gmail.com]
>> Sent: Monday, August 11, 2014 6:02 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Cluster results
>>
>> Hi,
>>
>> As in ptraj, reference structures can be specified with the
>> 'reference' command in cpptraj. In general, reference structures are
>> not needed for clustering. In your case you need one because you are
>> using a distance-based mask.
>>
>> -Dan
>>
>> On Mon, Aug 11, 2014 at 4:13 AM, Valentina Romano
>> <valentina.romano.unibas.ch> wrote:
>> > Hi
>> >
>> > I read details about the cluster command in cpptraj and it was not clear
>> to me how to specify what reference structure to use.
>> > In addition, what is the criterion to choose a structure as reference
>> structure when a MD trajectory is clustered?
>> >
>> > Thank you
>> > Best,
>> > valentina
>> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> > Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB
>> Swiss Institute of Bioinformatics
>> > Klingelbergstrasse 61 | CH-4056 Basel |
>> >
>> > Phone: +41 61 267 15 80
>> >
>> >
>> > ________________________________________
>> > From: Daniel Roe [daniel.r.roe.gmail.com]
>> > Sent: Friday, August 08, 2014 4:35 PM
>> > To: AMBER Mailing List
>> > Subject: Re: [AMBER] Cluster results
>> >
>> > OK, I think the issue is that you are trying to load your stripped
>> > cluster trajectory (i.e. trajectory without water) with your original
>> > topology. What you want to do is add something like 'outprefix nowat'
>> > to your 'strip' command. This will write out a stripped topology named
>> > nowat.<original topology name> that will correspond to your cluster
>> > trajectories/representatives. Also, unless you're using vmd on windows
>> > I really recommend using the netcdf format, 'clusterfmt netcdf', as
>> > this format is superior to the Amber ASCII trajectory format in every
>> > way.
>> >
>> > -Dan
>> >
>> > On Fri, Aug 8, 2014 at 8:30 AM, Valentina Romano
>> > <valentina.romano.unibas.ch> wrote:
>> >> The input was:
>> >>
>> >> trajin ../PknGAde_restr30ns.mdcrd
>> >> strip :WAT
>> >> cluster out cnumvtime.dat repout PknGAde_restr30ns.pdb repfmt pdb
>> clusterout PknGAde_restr30ns.nc
>> >> averagelinkage clusters 5 rms sieve 10 :247<:5.0
>> >>
>> >> I tried both (Amber coordinate and Amber coordinate with water box) and
>> it did not work.
>> >>
>> >> Vale
>> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> >> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB
>> Swiss Institute of Bioinformatics
>> >> Klingelbergstrasse 61 | CH-4056 Basel |
>> >>
>> >> Phone: +41 61 267 15 80
>> >>
>> >>
>> >> ________________________________________
>> >> From: Daniel Roe [daniel.r.roe.gmail.com]
>> >> Sent: Friday, August 08, 2014 4:25 PM
>> >> To: AMBER Mailing List
>> >> Subject: Re: [AMBER] Cluster results
>> >>
>> >> Hi,
>> >>
>> >> Without at least the input you gave to cpptraj (and ideally the
>> >> output) I can only guess, but perhaps you have box coordinates in your
>> >> amber trajectory and you are loading them as 'Amber coordinates'
>> >> instead of 'Amber coordinates with periodic box' (or vice versa).
>> >>
>> >> -Dan
>> >>
>> >> On Fri, Aug 8, 2014 at 8:10 AM, Valentina Romano
>> >> <valentina.romano.unibas.ch> wrote:
>> >>> Hi,
>> >>>
>> >>> Thank you.
>> >>>
>> >>> I have an additional question.
>> >>> I used cpptraj, as you suggested before and I got 5
>> <trajfileprefix>.cx. If I load them in VMD as AMber coordinates they looks
>> so strange?
>> >>> Do you why?
>> >>>
>> >>> Cheers,
>> >>> Valentina
>> >>>
>> >>>
>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> >>> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB
>> Swiss Institute of Bioinformatics
>> >>> Klingelbergstrasse 61 | CH-4056 Basel |
>> >>>
>> >>> Phone: +41 61 267 15 80
>> >>>
>> >>>
>> >>> ________________________________________
>> >>> From: Daniel Roe [daniel.r.roe.gmail.com]
>> >>> Sent: Friday, August 08, 2014 3:56 PM
>> >>> To: AMBER Mailing List
>> >>> Subject: Re: [AMBER] Cluster results
>> >>>
>> >>> Hi,
>> >>>
>> >>> On Fri, Aug 8, 2014 at 5:42 AM, Valentina Romano
>> >>> <valentina.romano.unibas.ch> wrote:
>> >>>> About the mask I used ( the correct one: :247<:5.0):
>> >>>> I would like to compare frames using the ligand (residue number 247)
>> and all residues within 5 A from it (<:5.0).
>> >>>> Is the ':247<:5.0' correct for this purpose?
>> >>>> If I do not specify any reference structure, is the first frame used
>> as reference by default? And, if yes, does it correct?
>> >>>
>> >>> The mask is right for what you want. You need to specify a reference
>> >>> in cpptraj for distance-based masks to work, and I believe the same is
>> >>> true in ptraj. It will "work" in the sense that the residues initially
>> >>> selected by that mask based on the reference structure will be the
>> >>> residues used for calculating the RMS metric throughout the
>> >>> trajectory. Whether it will work the way you want or not depends on
>> >>> how much the structure is changing in that region. For example, if
>> >>> there is some conformational shift near the beginning of the
>> >>> trajectory where one of the residues initially close to 247 moves a
>> >>> distance away, you will probably get consistently high RMSDs between
>> >>> structures and your clustering will be affected accordingly. The best
>> >>> way to ascertain the affect is to try it out and see. Pay close
>> >>> attention to what cluster sizes you get, what the representatives look
>> >>> like, etc. Clustering is usually more of an art form than a science,
>> >>> and it takes some playing around with it to get it right.
>> >>>
>> >>> Also, if you haven't already, check out this article on clustering:
>> >>> http://pubs.acs.org/doi/abs/10.1021/ct700119m
>> >>>
>> >>> Very in-depth but worth the time.
>> >>>
>> >>> -Dan
>> >>>
>> >>>>
>> >>>> Thank you.
>> >>>>
>> >>>> Best,
>> >>>> Vale
>> >>>>
>> >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> >>>> Valentina Romano | PhD Student | Biozentrum, University of Basel &
>> SIB Swiss Institute of Bioinformatics
>> >>>> Klingelbergstrasse 61 | CH-4056 Basel |
>> >>>>
>> >>>> Phone: +41 61 267 15 80
>> >>>>
>> >>>>
>> >>>> ________________________________________
>> >>>> From: Daniel Roe [daniel.r.roe.gmail.com]
>> >>>> Sent: Thursday, August 07, 2014 4:18 PM
>> >>>> To: AMBER Mailing List
>> >>>> Subject: Re: [AMBER] Cluster results
>> >>>>
>> >>>> Hi,
>> >>>>
>> >>>> A few comments based on your ptraj output. First, as Tom mentioned, in
>> >>>> ptraj if the 'all' cluster trajectory reached a certain file size it
>> >>>> was split up into several chunks to prevent the file size from
>> >>>> exceeding the file system's size limit, which years ago was commonly 4
>> >>>> GB (or even 2 GB). I think the limit encoded in ptraj is even smaller
>> >>>> than that though.
>> >>>>
>> >>>> The reason your cluster trajectories are so large is it appears you
>> >>>> are saving all atoms, solvent included. Unless you really need the
>> >>>> solvent for some reason I recommend that you strip the water prior to
>> >>>> clustering with 'strip :WAT'.
>> >>>>
>> >>>> Also, the mask you are using for RMS fitting appears malformed - it
>> >>>> looks like you tried to have a distance-dependent mask. What you have
>> >>>> is:
>> >>>>
>> >>>> :247 <:5.0
>> >>>>
>> >>>> The space means ':247' and '<:5.0' are treated as separate tokens. You
>> >>>> can see this in your output:
>> >>>>
>> >>>> MASK = :247
>> >>>> Mask [:247] represents 15 atoms
>> >>>>
>> >>>> To get this mask processed correctly you either need to remove the
>> >>>> space or enclose it in quotes. Also, this mask may not do what you
>> >>>> expect. Distance-dependent masks in ptraj and cpptraj are set up once
>> >>>> based on reference structures (except for the 'mask' action in
>> >>>> cpptraj). In your case since no atoms were stripped this might include
>> >>>> whatever water molecules are present in your reference, which will
>> >>>> likely have drifted far away in some frames leading to crazy RMSD
>> >>>> values. If you can elaborate on what your purpose was for using a
>> >>>> distance-dependent mask I may be able to make a better recommendation.
>> >>>>
>> >>>> Finally, I recommend you use cpptraj, which is faster, more stable,
>> >>>> and better-supported. The syntax for coordinate output in clustering
>> >>>> is slightly different, so you might use the following input:
>> >>>>
>> >>>> strip :WAT
>> >>>> cluster out cnumvtime.dat repout PknGAde_restr30ns.pdb repfmt pdb \
>> >>>> clusterout PknGAde_restr30ns.nc clusterfmt netcdf \
>> >>>> averagelinkage clusters 5 rms sieve 10 :247<:5.0
>> >>>>
>> >>>> Remember, for the distance dependent mask to work you will need to
>> >>>> load a reference. See the Amber 14 manual for full details on the
>> >>>> keywords.
>> >>>>
>> >>>> Hope this helps,
>> >>>>
>> >>>> -Dan
>> >>>>
>> >>>>
>> >>>> On Thu, Aug 7, 2014 at 2:34 AM, Valentina Romano
>> >>>> <valentina.romano.unibas.ch> wrote:
>> >>>>> Hi
>> >>>>>
>> >>>>> I got both <filename>.rep.c<#> and <filename>.avg.c<#>. In details,
>> I got 5 representative structures and 5 average structures ( 1 per each
>> cluster).
>> >>>>> Please find in attachment the ptraj output file I got.
>> >>>>> Hope this help to understand.
>> >>>>>
>> >>>>> Best,
>> >>>>> Vale
>> >>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> >>>>> Valentina Romano | PhD Student | Biozentrum, University of Basel &
>> SIB Swiss Institute of Bioinformatics
>> >>>>> Klingelbergstrasse 61 | CH-4056 Basel |
>> >>>>>
>> >>>>> Phone: +41 61 267 15 80
>> >>>>>
>> >>>>>
>> >>>>> ________________________________________
>> >>>>> From: Daniel Roe [daniel.r.roe.gmail.com]
>> >>>>> Sent: Wednesday, August 06, 2014 5:09 PM
>> >>>>> To: AMBER Mailing List
>> >>>>> Subject: Re: [AMBER] Cluster results
>> >>>>>
>> >>>>> Hi,
>> >>>>>
>> >>>>> Just to check, did you also get files <filename>.rep.c<#> and
>> >>>>> <filename>.avg.c<#> (for representative and average structures
>> >>>>> respectively)? The only way I can think of you getting files named
>> >>>>> <filename>.c<#>.X is if you chose a file format that writes multiple
>> >>>>> frames (like Amber restart or PDB etc). I think we would need to see
>> >>>>> your entire ptraj output to debug further.
>> >>>>>
>> >>>>> As Brian suggested, if you're just using averagelinkage you may want
>> >>>>> to try using cpptraj instead; it's faster and better-supported
>> >>>>> overall.
>> >>>>>
>> >>>>> -Dan
>> >>>>>
>> >>>>> On Wed, Aug 6, 2014 at 8:27 AM, Valentina Romano
>> >>>>> <valentina.romano.unibas.ch> wrote:
>> >>>>>> This is the cluster command I used:
>> >>>>>>
>> >>>>>> trajin ../PknGAde_md_rest20ns_reimage.mdcrd
>> >>>>>> cluster out PknGAde_restr20ns representative pdb average pdb all
>> amber averagelinkage clusters 5 rms sieve 10 :247 <:5.0
>> >>>>>>
>> >>>>>> Suggestions?
>> >>>>>>
>> >>>>>> vale
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> >>>>>> Valentina Romano | PhD Student | Biozentrum, University of Basel &
>> SIB Swiss Institute of Bioinformatics
>> >>>>>> Klingelbergstrasse 61 | CH-4056 Basel |
>> >>>>>>
>> >>>>>> Phone: +41 61 267 15 80
>> >>>>>>
>> >>>>>>
>> >>>>>> ________________________________________
>> >>>>>> From: Brian Radak [radak004.umn.edu]
>> >>>>>> Sent: Wednesday, August 06, 2014 3:37 PM
>> >>>>>> To: AMBER Mailing List
>> >>>>>> Subject: Re: [AMBER] Cluster results
>> >>>>>>
>> >>>>>> I think you'll have to provide the specific cluster command you
>> used if you
>> >>>>>> want help on this.
>> >>>>>>
>> >>>>>> Also, if I remember correctly, the cluster implementations in ptraj
>> and
>> >>>>>> cpptraj are a bit different, but the latter is still recommended.
>> >>>>>>
>> >>>>>> Regards,
>> >>>>>> Brian
>> >>>>>>
>> >>>>>>
>> >>>>>> On Wed, Aug 6, 2014 at 8:22 AM, Valentina Romano <
>> valentina.romano.unibas.ch
>> >>>>>>> wrote:
>> >>>>>>
>> >>>>>>> Dear Amber users
>> >>>>>>>
>> >>>>>>> I clustered a MD trajectory using the command cluster in ptraj. I
>> used 5
>> >>>>>>> as number of clusters.
>> >>>>>>>
>> >>>>>>> In addition to 5 filename.ci files (e.g. filename.c0, filename.c1
>> etc), I
>> >>>>>>> obtained additional files for each .ci file.
>> >>>>>>> For instance, in addition to filename.c0 I also obtained
>> flilename.c0.1,
>> >>>>>>> filename.c0.2 and so on.
>> >>>>>>>
>> >>>>>>> Anyone can explain me what these files are?
>> >>>>>>>
>> >>>>>>> Best,
>> >>>>>>> Valentina
>> >>>>>>>
>> >>>>>>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> >>>>>>> Valentina Romano | PhD Student | Biozentrum, University of Basel &
>> SIB
>> >>>>>>> Swiss Institute of Bioinformatics
>> >>>>>>> Klingelbergstrasse 61 | CH-4056 Basel |
>> >>>>>>>
>> >>>>>>> Phone: +41 61 267 15 80
>> >>>>>>>
>> >>>>>>> _______________________________________________
>> >>>>>>> AMBER mailing list
>> >>>>>>> AMBER.ambermd.org
>> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>> --
>> >>>>>> ================================ Current Address
>> =======================
>> >>>>>> Brian Radak :
>> BioMaPS
>> >>>>>> Institute for Quantitative Biology
>> >>>>>> PhD candidate - York Research Group : Rutgers, The State
>> >>>>>> University of New Jersey
>> >>>>>> University of Minnesota - Twin Cities : Center for
>> >>>>>> Integrative Proteomics Room 308
>> >>>>>> Graduate Program in Chemical Physics : 174 Frelinghuysen
>> Road,
>> >>>>>> Department of Chemistry : Piscataway,
>> NJ
>> >>>>>> 08854-8066
>> >>>>>> radak004.umn.edu :
>> >>>>>> ====================================================================
>> >>>>>> _______________________________________________
>> >>>>>> 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 201
>> >>>> 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)
>> >>
>> >> _______________________________________________
>> >> 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)
>>
>> _______________________________________________
>> 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
>>
> _______________________________________________
> 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
Received on Fri Aug 15 2014 - 13:30:03 PDT
