[gmx-users] Re: Gromacs analysis tools for Namd output

[Francesco Oteri]

Hu Paul,
it is possible the dl library (containing the function to dinamically 
loading libraries) is missed.
To confirm this hypotesis, try:
ldd path_g_rmsf

On my PC this is the output:

         linux-vdso.so.1 =>  (0x00007fffdddd6000)
         libgmxana.so.6 => /apps/gromacs/4.5.5/gnu/lib/libgmxana.so.6 
(0x00007f6e50994000)
         libmd.so.6 => /apps/gromacs/4.5.5/gnu/lib/libmd.so.6 
(0x00007f6e50529000)
         libxml2.so.2 => /usr/lib/libxml2.so.2 (0x00007f6e501a9000)
         libgmx.so.6 => /apps/gromacs/4.5.5/gnu/lib/libgmx.so.6 
(0x00007f6e4fbe6000)
*        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 
(0x00007f6e4f9e2000)*
         libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 
(0x00007f6e4f7c7000)
         libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6e4f542000)
         libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 
(0x00007f6e4f324000)
         libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6e4ef8f000)
         libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6e4ed77000)
         /lib64/ld-linux-x86-64.so.2 (0x00007f6e50de2000)

If you miss this library, try to instrall again gromacs including this 
library

Francesco

Il 07/02/2012 20:04, Kunze, Micha ha scritto:
> Hey Paul,
>
> cant help you with the plugin issue, but have you instead tried 
> loading the dcd trajectory into vmd and save it as trr?
>
> Cheers,
> Micha
>
> On 7 Feb 2012, at 18:18, "PAUL NEWMAN" <paulclizana at gmail.com 
> <mailto:paulclizana at gmail.com>> wrote:
>
>> Dear Gromacs users,
>>
>> This is my second email since I tried the previous advises and did 
>> NOT work.
>>
>> I want to use the Gromacs analysis tools for analyzing Namd output 
>> files (*.dcd files) I installed Gromacs 4.5.4 (64 bits) and it works 
>> well. In addition I installed VMD 1.9 (64 bits) and set up 
>> VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/   (Here it 
>> is located the  dcdplugin.so )
>>
>> I verified that VMD_PLUGIN_PATH is pointing out to the right folder. 
>> However when I run for example
>>
>> *g_rmsf_d -f file.dcd  -s file.pdb *
>>
>> I got the following error
>>
>> *The file format of file.dcd is not a known trajectory format to 
>> GROMACS. Please make sure that the file is a trajectory!
>>
>> GROMACS will now assume it to be a trajectory and will try to open it 
>> using the VMD plug-ins.* *
>> This will only work in case the VMD plugins are found and it is a 
>> trajectory format supported by VMD.
>>
>> No plugin for dcd found*
>>
>>
>> Can anyone tell me if Gromacs really works with the VMD pulgin?
>>
>> I will highly appreciate to know it so I can start looking for 
>> another alternatives.
>>
>> Thanks so much
>>
>>
>>
>> -- 
>> Cheers,
>>
>> Paul
>>
>>
>> -- 
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>

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