[gmx-users] Error in compiling GROMACS3.2.1

[raja]

> 
> That message is now outdated since there is an AMBER version for gmx 3.3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 That message is now outdated since there is an AMBER version for gmx 3.3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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-- 
  raja
  raja_28 at fastmail.us

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