Hi..
I listed all the zipped files separately as you said.
g_wham -bins 1000 pull1.pdo.gz pull2.pdo.gz pull3.pdo.gz pull4.pdo.gz
pull5.pdo.gz -temp 298 -o pmf.xvg
I still have the same problem.
:-) G R O M A C S (-:
GRoups of Organic Molecules in ACtion for Science
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_wham (-:
Option Filename Type Description
------------------------------------------------------------
-o pmf.xvg Output xvgr/xmgr file
-hist histo.xvg Output xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-min real 0 Minimum coordinate in profile
-max real 0 Maximum coordinate in profile
-bins int 1000 Number of bins in profile
-[no]prof bool yes Only calculate min and max
-temp real 298 Temperature
-[no]flip bool no Combine halves of profile
-tol real 0.01 Tolerance
Opening file pull1.pdo.gz.
-------------------------------------------------------
Program g_wham, VERSION 3.3.1
Source code file: gmx_wham.c, line: 90
Fatal error:
This does not appear to be a valid pdo file
-------------------------------------------------------
That is the error which I get....
Thank You for your input..
Also if it is not bothering you can you please send me the modified version
of g_wham by David Bostick else I shall check it once again as I couldn't
find it earlier.
Thanks,
SK
On 7/3/07, Lu Lanyuan <[EMAIL PROTECTED]> wrote:
I just zipped alll the *.pdo files seperately and listed them all when
using g_wham. It's like g_wham <options> pull1.pdo.gz pull2.pdo.gz ... In
the old gromacs versions like 3.1.4, the g_wham was broken and I was using
a version modifined by David Bostick. You can search the mailing list for
that information. I'm not sure whether the old problem of g_wham was fixed
in 3.3.1.
Lanyuan Lu
>From: "Sudha Mani Karra" <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
>Subject: Re: [gmx-users] g_wham and PMF problem
>Date: Tue, 3 Jul 2007 10:08:33 -0500
>
>Hi Mark,
> when I give only one file in the input for g_wham,
>
>g_wham -o pmf.xvg -hist pull1.pdo ,
>
>It asks me to give a series of inputs.The error which I get is
> :-) g_wham (-:
>
>Option Filename Type Description
>------------------------------------------------------------
> -o pmf.xvg Output xvgr/xmgr file
>-hist pull1.pdo.xvg Output xvgr/xmgr file
>
> Option Type Value Description
>------------------------------------------------------
> -[no]h bool no Print help info and quit
> -nice int 0 Set the nicelevel
> -[no]w bool no View output xvg, xpm, eps and pdb files
> -[no]xvgr bool yes Add specific codes (legends etc.) in the
>output
> xvg files for the xmgrace program
> -min real 0 Minimum coordinate in profile
> -max real 0 Maximum coordinate in profile
> -bins int 100 Number of bins in profile
> -[no]prof bool yes Only calculate min and max
> -temp real 298 Temperature
> -[no]flip bool no Combine halves of profile
> -tol real 0.01 Tolerance
>
>-------------------------------------------------------
>Program g_wham, VERSION 3.3.1
>Source code file: gmx_wham.c, line: 314
>
>Fatal error:
>You need to specify a series of pdo files as input
>---------------------------------------------------
>
>Appreciate your help.Thanks,
>SK
>
>
>
>
>
>
>
>On 7/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
>>
>> > Hey Mark,
>> > Appreciate your immediate response.You can find the
>>input and
>> > the
>> > error below:
>> > g_wham -o pmf.xvg -hist pull1.pdo pull2.pdo pull3.pdo pull4.pdo
>>pull5.pdo
>>
>>g_wham -h suggests that -hist won't accept multiple input files.
>>Only a
>>few GROMACS utilities will do magic concatenation for you. Have a
>>look at
>>the file format and see what you need to do with a text editor or
>>command
>>line tools.
>>
>> > Opening file pull2.pdo.
>> >
>> > gunzip: stdin: not in gzip format
>> > -------------------------------------------------------
>> > Program g_wham, VERSION 3.3.1
>> > Source code file: gmx_wham.c, line: 90
>> >
>> > Fatal error:
>> > This does not appear to be a valid pdo file
>> > -------------------------------------------------------
>>
>>Does g_wham -o pmf.xvg -hist pull1.pdo work?
>>
>>Mark
>>
>>_______________________________________________
>>gmx-users mailing list gmx-users@gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to [EMAIL PROTECTED]
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>_______________________________________________
>gmx-users mailing list gmx-users@gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before
posting!
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to [EMAIL PROTECTED]
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_________________________________________________________________
与联机的朋友进行交流，请使用 Live Messenger;
http://get.live.com/messenger/overview
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
