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)
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Received on Fri Jun 21 2013 - 08:30:02 PDT
