Hi,
I can't reproduce the error you are seeing. Here is the input I am
using for my test case:
INITIAL CLUSTERING WITH SIEVE:
trajin ../tz2.nc
cluster out ptrajcluster representative pdb average pdb averagelinkage
sieve 2 clusters 5 rms mass :2-11
SECOND DBI CLUSTERING:
trajin ../tz2.nc
cluster out ptrajcluster representative pdb average pdb dbi clusters 5
rms mass :2-11
I get warnings like this:
WARNING in ReadSymMatrix(): Existing file PairwiseDistances is not
correct. Need more data.
Which I think is innocuous; its just ptraj acknowledging the existing
pairwise matrix was calculated with sieving; I believe the necessary
distances are recalculated. My 'ptrajcluster.txt' file gets updated
with the DBI/pSF values at the end.
Make sure the "cluster40C.1_1N8R_means.txt" file exists, that you are
really using the most up to date ptraj, and as a last resort try
removing the 'average pdb' and 'representative pdb' arguments from the
'dbi' cluster command. If it still doesn't work please send me
(off-list) your complete ptraj output. Thanks.
-Dan
On Fri, Jun 21, 2013 at 9:18 AM, Amparo Garcia Lopez
<Amparo.GarciaLopez.unige.ch> wrote:
> thanks for your prompt reply, Dan.
>
> this is what happens:
> 1)
> cluster out cluster40C.1_1N8R_means representative pdb \
> average pdb dbi sieve 100 clusters 15 rms mass :2-20
>
> PTRAJ: cluster out cluster40C.1_1N8R_means representative pdb average dbi sieve 100 clusters 15 rms mass :2-20
> WARNING: invalid file format sieve!
> MASK = 100
> ERROR in tokenize(): wrong syntax
>
> (it aborts here)
>
> 2)
> cluster out cluster40C.1_1N8R_means representative pdb \
> average pdb dbi clusters 15 rms mass :2-20
>
> PTRAJ: cluster out cluster40C.1_1N8R_means representative pdb average dbi clusters 15 rms mass :2-20
> WARNING: invalid file format clusters!
> WARNING in ptraj(), cluster: Must specify either 'clusters' or 'epsilon'.
> [No output trajectory specified (trajout)]
> ../../40C_1N8R1-15.1.dry.trj: 488958 frames.
>
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 488958 frames.
> Summary of I/O and actions follows:
>
> INPUT COORDINATE FILES
> File (../../40C_1N8R1-15.1.dry.trj) is an AMBER trajectory with 488958 sets
>
> NO OUTPUT COORDINATE FILE WAS SPECIFIED
>
> NO ACTIONS WERE SPECIFIED
> openTraj(): Opening ../../40C_1N8R1-15.1.dry.trj
>
> (it goes on reading the trajectory, but the cluster.txt file still has no DBI or pSF values)
>
> Any other ideas?
>
> Thanks!
> Amparo
>
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: 21 June 2013 16:30
> To: AMBER Mailing List
> Subject: Re: [AMBER] post-clustering calculation of DBI and pSF
>
> Hi,
>
> On Fri, Jun 21, 2013 at 7:34 AM, Amparo Garcia Lopez
> <Amparo.GarciaLopez.unige.ch> wrote:
>> cluster out cluster40C.1_1N8R_means representative pdb \
>> average pdb DBI sieve 100 clusters 15 rms mass :2-20
>
> Try 'dbi' (lower case) instead of 'DBI'.
>
> -Dan
>
> --
> -------------------------
> 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) 585-9119 (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) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 21 2013 - 09:30:09 PDT
