[gmx-users] Error in compiling GROMACS3.2.1

[David van der Spoel]

raja wrote:
>> That message is now outdated since there is an AMBER version for gmx 3.3
>>
>>
> 
> Dear Mr.David and other gmxions,
> Thanks for your mail. but why the following errors is occuring when I
> use AMBER forcefield for RNA
> of my interest. 
> This is the following error occours when I run pdb2gmx in gromacs3.3
> 
> #####################################################################
> Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99.rtp
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Reading 1U8D.pdb...
> Read 'XPT-PBUX MRNA', 1426 atoms
> Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
> 26 out of 26 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 67 residues with 1426 atoms
> 
>   chain  #res #atoms
>   1 'A'    67   1426
> 
> All occupancies are one
> Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99.atp
> Atomtype 73
> Reading residue database... (ffamber99)
> Opening library file /usr/local/gromacs/share/gromacs/top/ffamber99.rtp
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3
> Source code file: resall.c, line: 331
> 
> Fatal error:
> in .rtp file at line:
> -------------------------------------------------------
> 
> "Here's Another Useful Quote" (S. Boot)
> 
> ##########################################################################################
> 
> 
> Thanks !
> B.Nataraj
> 
> 
> 
> On Fri, 03 Feb 2006 10:40:02 +0100, "David van der Spoel"
> <spoel at xray.bmc.uu.se> said:
>> raja wrote:
>>> Dear GMXIONs,
>>>        There is need for me to install GROMACS3.2.1 for its
>>>        compatiability in conversting RNA pdb file to gmx file 
>>> (pdb2gmx) as per the reference from GROMACS user forum
>>> (http://www.gromacs.org/pipermail/gmx-users/2005-October/017682.html) .
>> That message is now outdated since there is an AMBER version for gmx 3.3
>>
>>
>>> For that purpose I tried to install GROMACS3.2.1 , More I am having
>>> installed programs of fftw3 for both double and single precision and
>>> GROMACS3.3 in my system.(Hereby I explained why I wanted the previous
>>> version to avoid any suggestions from your side to install latest
>>> version)
>>>
>>> But the problem is when I try to compile GROMACS3.2.1 by make command ,
>>> I ended up in following error...
>>> ###############################################################################################
>>> til.o topdirs.o grompp.o ../mdlib/libmd.la ../gmxlib/libgmx.la 
>>> -L/usr/X11R6/l
>>>  -lsrfftw -lsfftw -lm   -lSM -lICE -lX11  -L/usr/lib -lxml2 -lz -liconv
>>>  -lm
>>> cc -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
>>> -malign-doubl
>>> -funroll-all-loops -I/usr/include/libxml2 -o grompp.exe topio.o
>>> toppush.o topc
>>> .o topshake.o convparm.o tomorse.o sorting.o splitter.o dum_parm.o
>>> readir.o ad
>>> par.o topexcl.o toputil.o topdirs.o grompp.o  -L/usr/local/fftw/lib
>>> ../mdlib/.
>>> bs/libmd.a -L/usr/X11R6/lib -L/usr/lib ../gmxlib/.libs/libgmx.a -lsrfftw
>>> -lsff
>>>  -lSM -lICE -lX11 .libs/libimp-cygxml2-2.a -lz .libs/libimp-cygiconv-2.a
>>> /usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld:
>>> cannot fi
>>>  -lz
>>> collect2: ld returned 1 exit status
>>> make[3]: *** [grompp.exe] Error 1
>>>
>>> ##################################################################################################
>>>
>>> >From the reference of user forum I also tried the configuration step by
>>> this command
>>> *******************************************************
>>>> ./configure --without-motif-includes 
>>> *******************************************************
>>>
>>> Again the same problem 
>>>
>>> Thanks !
>>> B.Nataraj
>>
>> -- 
>> David.
>> ________________________________________________________________________
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> phone:  46 18 471 4205          fax: 46 18 511 755
>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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try running with -debug. It will produce a pdb2gmx.log file with extra info.

Is this indeed the gromacs 3.3 compatible version of the amber force field?

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++