Re: [gmx-users] Read mdcrd from AMBER --- Error Message

2012-03-08 Thread francesco oteri 
Hi Catherine,
you should install any gromacs *4.5.x*, and then you can use gromacs
with each trajectory supported by VMD because gromacs is able to use VMD plugin
to
perform trajectory reading.
Basically:
1) Install the latest gromacs version
2) Install VMD
3) Set the variable VMD_PLUGIN_PATH to contain the complete path of the
molfile vmd directory.
   In my case, for example:  VMD_PLUGIN_PATH=/apps/vmd/1.9/**lib/vmd
/plugins/LINUXAMD64/**molfile

Francesco

Il giorno 08 marzo 2012 17:40, a a pat...@hotmail.com ha scritto:

  Dear Sir/Madam,

 I learnt that we can use mdcrd from AMBER directly.

 I have used the following commands.

 /share1/gromacs/bin/g_covar -s xxx.pdb -f xxx.mdcrd -o -v

 An error message was obtained.

 Program g_covar, VERSION 4.0.7
 Source code file: gmxfio.c, line: 737

 Can not open file:
 md0.mdcrd.xtc

 Did I do anything wrong?

 Best regards,

 Catherine



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-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] Read mdcrd from AMBER --- Error Message

2012-03-08 Thread Mark Abraham 

On 9/03/2012 3:40 AM, a a wrote:

Dear Sir/Madam,

I learnt that we can use mdcrd from AMBER directly.

I have used the following commands.

/share1/gromacs/bin/g_covar -s xxx.pdb -f xxx.mdcrd -o -v

An error message was obtained.

Program g_covar, VERSION 4.0.7
Source code file: gmxfio.c, line: 737

Can not open file:
md0.mdcrd.xtc

Did I do anything wrong?


Did you read and follow the link I gave you? 
http://www.gromacs.org/Documentation/How-tos/Using_VMD_plugins_to_read_trajectory_formats_not_native_to_GROMACS. 
The error you cite means GROMACS did not find your VMD plugins. You 
should not need to update GROMACS, per someone else's suggestion.


When asking for help, please copy and paste your full command line. 
Details and precision are usually important, though not here.


Mark
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