[gmx-users] add timestamp to frames: conclusion
barrett
barrett at biop.ox.ac.uk
Fri Jul 18 10:17:01 CEST 2003
Thanks to everyone. Both Graham and Patrick's methods worked.
Method 1: be more explicit about where the molecules start and finish
---------------------------------------------------------------------
Add 'ENDMDL' to the end of each PDB frame and concatenate them by hand
(into e.g. catted.pdb) with END at the end of the PDB then:
trjconv -f catted.pdb -o catted.xtc -t0 0 -timestep 1
Method 2: make one good .xtc and append everything to that
---------------------------------------------------------
It your two PDB files are x.pb and y.pdb
trjconv -f x.pdb -o x.xtc -t0 1
trjconv -f y.pdb -o y.xtc -t0 2
cp x.xtc catted.xtc
trjconv -app -o catted.xtc -f y.xtc
Both of these methods leave you with nice trajectories with timestamps
which can be processed by g_covar
Thanks again
Paul
-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
On Behalf Of barrett
Sent: 16 July 2003 12:34
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] add timestamp to frames
Thanks for the reply David.
This doesn't work though: I had tried -settime.
More generally the problem can be restated thus:
Typing:
> trjconv -f x.pdb -o x.xtc -t0 1
> trjconv -f y.pdb -o y.xtc -t0 2
then the subsequent command...
> trjcat -o out.xtc x.xtc y.xtc
(with or without -settime and with -b and -e set to various
combinations)
gives the following error:
:
:
Last frame 0 time 1.000
Fatal error:
Couldn't read time from second frame.
(there *is* no second frame in either .xtc)
have any kind souls out there got any ideas on how to fix this?
Cheers
Paul
-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
On Behalf Of David
Sent: 15 July 2003 17:34
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] add timestamp to frames
On Tue, 2003-07-15 at 17:29, barrett wrote:
> Hi
>
>
>
> Summary:
>
> how do you add timestamps to a set of pdbs in a trajectory saved from
> VMD.
>
>
>
> Background:
>
> I have a concatenated set of pdb files without any time stamps on the
> frames.
>
> I want to process them with g_covar. However g_covar dies immediately
> complaining about too many iterations in jacobi.
>
> I think this is because it is trying to read the timeframe and cannot
> find it.
>
>
>
> THEREFORE: I want to add timestamps to the frames of the trajectory.
>
>
>
> I tried taking the individual frames as PDB files and then:
>
>
>
> trjconv -f X.pdb -o X.xtc -t0 1
>
> trjconv -f Y.pdb -o Y.xtc -t0 2
>
> etc..
>
>
>
> followed by
>
>
>
> trjcat -o ensemble.xtc *aligned.xtc
This works for me (using CVS code)
An alternative is to trjcat the pdb files directly if necessary with the
-settime option
remember the -h flag is your friend... (I don't know all those options
either)
>
>
>
> but this failed:
>
>
>
> Last frame 0 time 1.000
>
> Fatal error:
>
> Couldn't read time from second frame.
>
>
>
> Suggestions very much appreciated
>
>
>
> Paul
>
>
>
> Dr Paul Barrett
>
> Laboratory of Molecular Biophysics
>
> Department of Biochemistry
>
> University of Oxford
>
> Oxford
>
> OX1 3QU
>
>
>
> Tel 01865 275191
>
> Fax 01865 275182
>
>
>
>
> _______________________________________________ gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post
> (un)subscribe requests to the list. Use the www interface or send it
> to gmx-users-request at gromacs.org.
>
------------------------------------------------------------------------
-------- Return-Path: Received: by biop.ox.ac.uk (MX V4.2 AXP) with
SITE; Mon, 14 Jul 2003 12:33:06 +0100 Received: from oxmail.ox.ac.uk by
nutmeg.biop.ox.ac.uk (MX V4.2 AXP) with SMTP; Mon, 14 Jul 2003 12:33:05
+0100 Received: from hawk.theophys.kth.se ([130.237.25.19]) by
oxmail.ox.ac.uk with smtp (Exim 4.14) id 19c1Zn-0000x9-AQ for
barrett at biop.ox.ac.uk; Mon, 14 Jul 2003 12:33:03 +0100 Received: (qmail
3352 invoked from network); 14 Jul 2003 11:33:02 -0000 Received: from
localhost (HELO hawk.theophys.kth.se) (127.0.0.1) by 0 with SMTP; 14 Jul
2003 11:33:02 -0000 Received: (qmail 3316 invoked from network); 14 Jul
2003 11:32:34 -0000 Received: from bay7-f92.bay7.hotmail.com (HELO
hotmail.com) (64.4.11.92) by 0 with SMTP; 14 Jul 2003 11:32:34 -0000
Received: from mail pickup service by hotmail.com with Microsoft
SMTPSVC; Mon, 14 Jul 2003 04:32:11 -0700 Received: from 202.127.19.80 by
by7fd.bay7.hotmai!
l.msn.com with HTTP; Mon, 14 Jul 2003 11:32:10 GMT Message-ID:
--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
------------------------------------------------------------------------
--------
Return-Path: <gmx-users-admin at gromacs.org>
Received: by biop.ox.ac.uk (MX V4.2 AXP) with SITE; Tue, 15 Jul 2003
17:32:12
+0100
Received: from oxmail.ox.ac.uk by nutmeg.biop.ox.ac.uk (MX V4.2 AXP)
with SMTP;
Tue, 15 Jul 2003 17:32:11 +0100
Received: from webmail.theophys.kth.se ([130.237.25.19]
helo=hawk.theophys.kth.se) by oxmail.ox.ac.uk with smtp (Exim
4.14)
id 19cSip-0003ub-5Y for barrett at biop.ox.ac.uk; Tue, 15 Jul
2003
17:32:11 +0100
Received: (qmail 26277 invoked from network); 15 Jul 2003 16:32:02 -0000
Received: from localhost (HELO hawk.theophys.kth.se) (127.0.0.1) by 0
with
SMTP; 15 Jul 2003 16:32:02 -0000
Received: (qmail 26241 invoked from network); 15 Jul 2003 16:31:45 -0000
Received: from h28n2fls34o1123.telia.com (81.224.175.28) by 0 with SMTP;
15 Jul
2003 16:31:45 -0000
Received: from h28n2fls34o1123.telia.com (localhost.localdomain
[127.0.0.1]) by
h28n2fls34o1123.telia.com (8.12.8/8.12.8) with ESMTP id
h6FGYWb4002417 for <gmx-users at gromacs.org>; Tue, 15 Jul 2003
18:34:32
+0200
Received: (from spoel at localhost) by h28n2fls34o1123.telia.com
(8.12.8/8.12.8/Submit) id h6FGXld5002410 for
gmx-users at gromacs.org;
Tue, 15 Jul 2003 18:33:47 +0200
Message-ID: <1058286826.1742.22.camel at h28n2fls34o1123.telia.com>
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
------------------------------------------------------------------------
--------
Return-Path: <gmx-users-admin at gromacs.org>
Received: by biop.ox.ac.uk (MX V4.2 AXP) with SITE; Wed, 16 Jul 2003
12:39:02
+0100
Received: from oxmail.ox.ac.uk by nutmeg.biop.ox.ac.uk (MX V4.2 AXP)
with SMTP;
Wed, 16 Jul 2003 12:39:01 +0100
Received: from hawk.theophys.kth.se ([130.237.25.19]) by oxmail.ox.ac.uk
with
smtp (Exim 4.14) id 19ckcf-0000kR-DA for
barrett at biop.ox.ac.uk; Wed,
16 Jul 2003 12:39:01 +0100
Received: (qmail 6273 invoked from network); 16 Jul 2003 11:39:02 -0000
Received: from localhost (HELO hawk.theophys.kth.se) (127.0.0.1) by 0
with
SMTP; 16 Jul 2003 11:39:02 -0000
Received: (qmail 6239 invoked from network); 16 Jul 2003 11:38:49 -0000
Received: from oxmail1.ox.ac.uk (HELO oxmail.ox.ac.uk) (129.67.1.2) by 0
with
SMTP; 16 Jul 2003 11:38:49 -0000
Received: from fennel.biop.ox.ac.uk ([163.1.16.174]) by oxmail.ox.ac.uk
with
smtp (Exim 4.14) id 19ckc8-0003tj-5L for
gmx-users at gromacs.org; Wed,
16 Jul 2003 12:38:28 +0100
Received: by biop.ox.ac.uk (MX V4.2 AXP) with SITE; Wed, 16 Jul 2003
12:38:28
+0100
Received: from universipasjlz (cycle) by nutmeg.biop.ox.ac.uk (MX V4.2
AXP)
with SMTP; Wed, 16 Jul 2003 12:38:27 +0100
Message-ID: <001101c34b8e$370ca280$81e810ac at universipasjlz>
More information about the gromacs.org_gmx-users
mailing list