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
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> >>
> >>
> >> --
> >> -------------------------
> >> 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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> >
> >
> >
> > --
> > -------------------------
> > 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
> >
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>
>
>
> --
> -------------------------
> 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
>
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>
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Received on Wed Aug 13 2014 - 07:30:02 PDT
