RE: [gmx-users] pdb2gmx with DNA

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, July 09, 2010 8:08 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] pdb2gmx with DNA Patargias, George wrote: Thanks for your reply

[gmx-users] Missing sugar atom in CHARMM dna.rtp

Hi In the gromacs git version, I noticed that the sugar atom O2' is missing from the dna.rtp file... Best wishes George-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

[gmx-users] pdb2gmx with DNA

Thanks for your reply Justin. I am trying to generate a topology dor a dna structure using the charmm dna.rtp I have renamed the residue name to DA , DG etc. I have also set DA5 and DC3 for the 5' and 3' ends I got this error Fatal error: atom N not found in buiding block 2DG while

RE: [gmx-users] Compiling problems on MacOS X 10.6.4

Thanks for your reply. The output from nm -arch i386 /opt/local/lib/libxml2.a | head is nm: file: /opt/local/lib/libxml2.a does not contain architecture: i386 and from nm -arch x86_64 /opt/local/lib/libxml2.a | head /opt/local/lib/libxml2.a(SAX.o): 3050 s EH_frame1 02a0

RE: [gmx-users] Compiling problems on MacOS X 10.6.4

Sorry, I forgot to post the output of file src/*/*.o | head src/gmxlib/3dview.o: Mach-O object i386 src/gmxlib/atomprop.o:Mach-O object i386 src/gmxlib/bondfree.o:Mach-O object i386 src/gmxlib/calcgrid.o:Mach-O

RE: [gmx-users] Compiling problems on MacOS X 10.6.4

could pass the following flags to configure to see if it cures your problem: CFLAGS=-m64 -std=gnu99 -O3 Hope this helps, Rui Rodrigues On Thu, 8 Jul 2010 10:14:16 -0400, Patargias, George wrote Sorry, I forgot to post the output of file src/*/*.o | head src/gmxlib/3dview.o

[gmx-users] Compiling problems on MacOS X 10.6.4

Hi I m trying to compile the gmx development version (from git) on MacOX (Darwin kernel) The configure is successful but after I enter make and after lots of output I get the following: ld: warning: in /opt/local/lib/libxml2.a, file was built for unsupported file format which is not the