Hi Dan
Thank you for your answer, it helped a lot.
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?
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
Received on Fri Aug 08 2014 - 05:00:02 PDT
