From: Philip Fowler (p.w.fowler_at_qmul.ac.uk)
Date: Tue Jun 28 2005 - 09:27:06 CDT
If I have use the second set of vmd-1.8.1 plugins then I get the
following error:
volta 334% make
gcc -Wall -O3 -fomit-frame-pointer -march=i686 -pipe
-I/home/philip/packages/catdcd-3.0/plugins-1.8.1b/include
-I/home/philip/packages/catdcd-3.0/plugins-1.8.1b/LINUX/molfile catdcd.c
-L/home/philip/packages/catdcd-3.0/plugins-1.8.1b/LINUX/molfile
-lmolfile_plugin -o cattrr
/home/philip/packages/catdcd-3.0/plugins-1.8.1b/LINUX/molfile/
libmolfile_plugin.a(dcdplugin-s.o)
(.text+0x150d): In function `read_next_timestep':
: undefined reference to `acos'
/home/philip/packages/catdcd-3.0/plugins-1.8.1b/LINUX/molfile/
libmolfile_plugin.a(dcdplugin-s.o)
(.text+0x152d): In function `read_next_timestep':
: undefined reference to `acos'
/home/philip/packages/catdcd-3.0/plugins-1.8.1b/LINUX/molfile/
libmolfile_plugin.a(dcdplugin-s.o)
(.text+0x1550): In function `read_next_timestep':
: undefined reference to `acos'
collect2: ld returned 1 exit status
make: *** [cattrr] Error 1
Compiling with an older set works, but then DCDunitcell is not
transferred.
Your binary works though! What did you do differently?
--Phil
> Phil,
>
> On Tuesday 28 June 2005 14:18, Philip Fowler wrote:
>
>> I have recompiled CatDCD 3.0 from the source code and I found that
>> you must specify in the makefile either the vmd 1.8 (released
>> 2/14/2003) or the first set of vmd 1.8.1 plugins (released 7/3/2003)
>> for the compilation to work. Newer versions will not compile.
>>
>
> This is, I believe, the very heart of the issue: IIRC, the ability
> to write
> unit cell information was added to VMD's dcd plugin in a fairly recent
> version.
> So you have to make it compile on your system, but that should be
> possible.
> Can you tell me more about the problems you have when compiling?
>
> In the meantime, you might want to try the attached Linux IA32 binary.
>
> Jerome
>
>
>
>> But, my new shiny version of catdcd still does not retain dcdunitcell
>> info in the resultant dcd files. The input dcd files do have this
>> info and it can be retrieved from within VMD1.8.3 but any catdcd'ed
>> dcd (with or without striding) does not (a,b,c are all set to 1.000).
>>
>> Does anyone have any ideas?
>>
>> --Phil
>>
>>
>>> Hi Phil,
>>>
>>> I have had this problem in the past. In the end I managed to fix it
>>> by recompiling CatDCD from the source code, which was (from memory)
>>> available at www.ks.uiuc.edu. Why it didn't work the first time is
>>> beyond me.
>>>
>>> Anyway, hope this helps, and good luck.
>>>
>>> Best regards,
>>> Ben Roberts
>>>
>>> --------------------------------------------------------------------
>>> -
>>> Benjamin P. Roberts, B.Sc.(Hons)
>>> Ph.D. Student
>>>
>>> Department of Medicinal Chemistry
>>> Victorian College of Pharmacy (Monash University)
>>> 381 Royal Parade, Parkville VIC 3052, Australia
>>>
>>> Phone +61 3 9903 9674 | Fax +61 3 9903 9582 | Mobile +61 401 784 940
>>> --------------------------------------------------------------------
>>> -
>>>
>
> --
> Jérôme Hénin
> Equipe de Dynamique des Assemblages Membranaires
> Université Henri Poincaré / CNRS
> Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 87
> http://www.edam.uhp-nancy.fr/
>
> <catdcd.gz>
>
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