From: Ben Roberts (Ben.P.Roberts_at_vcp.monash.edu.au)
Date: Tue Jun 28 2005 - 18:27:07 CDT
Hi Phil,
Now that I see this, I remember I had the same problem.
What you need to do is add the text " -lm" (no quotes) to the end of the
CFLAGS line in your Makefile. This will build in the maths library which
includes acos etc.
Hope this works, and good luck.
Ben
Philip Fowler wrote:
> 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>
>>
>
>
-- 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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:38 CST