[gmx-users] error while concatenating .xtc files
Hi there! I was wondering if one can reply me about error that i m getting. while concatenating .xtc file having both solvent and protein following error is shown. Continue writing frames from extend4ns.xtc t=2000 ps, frame=4000 Reading frame 540 time 2270.000 Fatal error: Magic Number Error in XTC file (read 4021, should be 1995) but no error was obseverd while concatenating .xtc file having only protein Sincerely manmohan Manmohan Singh Gurjar M.Sc.Biotechnology(IInd year) School of Bioscience and Bioengineering IIT Powai Mumbai-400076 e-mail [EMAIL PROTECTED] [EMAIL PROTECTED] mobile- 9819850822 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analysis programs and PBC.
Daniela S. Mueller wrote: [...] If you have one chain, you don't have to worry about jumps. In addition, from the cases that I have encountered, you can have ligands and/or cofactors (non-covalently) bound to an enzyme, and e.g. counter-ions for which you want to analyze the position in relation to the protein. -- Groetjes, Anton * NOTE: New Affiliation, Phone Fax numbers (below) * _ ___ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 | | | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ | | | If You See Me Getting High, Knock Me Down (RHCP)| |_|___| ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_energy average --- bug?
Dear all, Looking at xmgrace graphics of temperature in function of time I clearly observe that the temperature in my 200,0 ps simulation was almost always between 261 K and 263,5K. Looking then the file md_T.xvg (file of temperature values during the time, that I got using g_energy), only the 0,1 first ps had different values next to 280 K, and all the other values where between 261 K and 263,5K. That is the very beggining, it should not affect that much the average. However, the average that I got from g_energy was 264,694 K. I really can not understand why this difference, it should be some value between 261 K and 263,5K. Is it a bug from g_energy? Should I trust in this average even knowing that the temperature accordind to the temperature file didn´t reached this value?? I wait for kind informations. Thanks for your attention, Best regards, Fernando Mattio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] steered MD
Dear all, I was trying to pull a ligand from a protein using AFM pulling option of Gromacs 3.3 but seems to be that it does not care about parameters that I specify in pull.ppa file. In particular, in spite of the fact that I may write to the input file coordinates of the unit vector describing the direction of pulling, gromacs does it in its own way in the direction of axis connecting centers of mass of reference and pulled groups AND not in the direction indicated in *.ppa file. I tried also do not indicate the reference group, thinking that it may work if pulling will be in absolute coordinates but I failed again because program just connected center of mass of the pulled group and point with coordinates (0 0 0).. Does someone know how to make it working? Thanks, Kamil ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ligand in vacuum trajectories (PRODRG)
Quoting Dariusz Plewczynski [EMAIL PROTECTED]: Dear Sirs, I have a problem with running the short simulation with GROMACS. I have a structure for a small ligand (drg.pdb after cleaning with PRODRG). For this ligand I have run PRODRG in order to get drg.gro file and drg.itp topology file. I have edited the drg.top in order to include drg.itp as #include. My goal is to run simulation in vacuum (no water) - with only ligand (!). No protein also. I have tried to run it but I am getting error message. It seem that GROMACS does not read my topology file. What I am doing wrong ? grompp -f em.mdp -c drg.gro -p drg.top -o drg.tpr Results: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations processing coordinates... Fatal error: number of coordinates in coordinate file (drg.gro, 25) does not match topology (drg.top, 0) You need to input the itp file generated by PRODRG of your drug into your drg.top file. do that by #include /your filepathway/drg.itp Regards Dariusz -- Farid Sa'adedin Membrane Biophysics Laboratory Department of Veterinary Biomedical Sciences College of Medicine Veterinary Medicine Royal (Dick) School of Veterinary Studies University of Edinburgh Summerhall Edinburgh EH9 1QH SCOTLAND ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Compilation problem on SGI ORIGIN 3800
David van der Spoel a écrit : Patrick Fuchs wrote: Hi gmx users, I'm trying to compile gromacs in // on an SGI ORIGIN 3800. For the monoCPU version it went well (thanks to very good advices on previous E-mails of the gmx list), but for the parallel version, I encountered a problem. Here are the steps I followed : setenv CPPFLAGS -I/opt/mpt/1.4.0.3/usr/include -I/usr/local/include setenv LDFLAGS -L/opt/mpt/1.4.0.3/usr/lib -L/usr/local/lib/fftw2.1.5/lib32 setenv LIBS -lmpi ./configure --enable-mpi --prefix=/home/fuchs/software/gromacs --program-suffix=_mpi --disable-float --disable-fortran --disable-nice - This step went OK make mdrun - at the beginning it went OK ... (cd ./src/kernel make mdrun ; exit 0) /bin/sh ../../libtool --mode=link mpicc -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -I/usr/freeware/include/libxml2 -L/opt/mpt/1.4.0.3/usr/lib -L/usr/local/lib/fftw2.1.5/lib32 -woff 84 -o mdrun glaasje.o gctio.o init_sh.o ionize.o do_gct.o relax_sh.o xutils.o md.o mdrun.o genalg.o ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la -lnsl -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw -lm -lmpi -lXm -lXt -lSM -lICE -lXext -lX11 -L/usr/freeware/lib32 -lxml2 -lz -lm libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/librfftw_mpi.la' was moved. This might be a problem. libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/libfftw_mpi.la' was moved. libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/librfftw.la' was moved.libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/libfftw.la' was moved. libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/librfftw_mpi.la' was moved. libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/libfftw_mpi.la' was moved. libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/librfftw.la' was moved.libtool: link: warning: library `/usr/local/lib/fftw2.1.5/lib32/libfftw.la' was moved. mpicc -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -I/usr/freeware/include/libxml2 -woff 84 -o mdrun glaasje.o gctio.o init_sh.o ionize.o do_gct.o relax_sh.o xutils.o md.o mdrun.o genalg.o -L/opt/mpt/1.4.0.3/usr/lib -L/usr/local/lib/fftw2.1.5/lib32 ../mdlib/.libs/libmd_mpi_d.a -L/usr/freeware/lib32 ../gmxlib/.libs/libgmx_mpi_d.a -lnsl /usr/local/lib/fftw2.1.5/lib32/librfftw_mpi.a /usr/local/lib/fftw2.1.5/lib32/libfftw_mpi.a /usr/local/lib/fftw2.1.5/lib32/librfftw.a /usr/local/lib/fftw2.1.5/lib32/libfftw.a -lmpi -lXm -lXt -lSM -lICE -lXext -lX11 -lxml2 -lz -lm cc: Warning: -OPT options are ignored cc: Warning: -OPT options are ignored cc: Warning: -SWP options are ignored cc: Warning: -OPT options are ignored uld: Object file format error in: glaasje.o: bad symbolic header (magic number) Something wrong with this file, delete it. *** Error code 1 (bu21) *** Error code 1 (bu21) I didn't find any similar case in the mailing list, and I'm wondering where could it come from. Does someone have an idea on how to fix that ? Thanks ! Patrick Could it be that you have restarted the compilation with differen flags? In that case you will have to do make distclean On SGI machines it has always been a problem to install the compilers, this problem is however hard to distinguish from others. You might want to start from scratch if make distclean doesn't do it. Thank you David, I made a distclean and then used the following : setenv CPPFLAGS -I/opt/mpt/1.4.0.3/usr/include -I/usr/local/include setenv LDFLAGS -L/opt/mpt/1.4.0.3/usr/lib -L/usr/local/lib/fftw2.1.5/lib32 setenv LIBS -lmpi setenv MPICC cc ./configure --enable-mpi --prefix=/home/fuchs/software/gromacs --program-suffix=_mpi --disable-float --disable-nice make mdrun And it worked ! The thing missing was the line 'setenv MPICC cc', and that makes all the difference. The option --disable-fortran has no effect wether it's used or not, as long as 'setenv MPICC cc' has been set. Ciao, Patrick -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
