Re: [gmx-users] How can i know if the protein swell during the MD simulation?
How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar > Hi, > > Well, I think 'swelling' is unambiguously, though roughly, defined as > 'growing larger', which suggests that you'd have to look for an > increase in volume. But how to do that, how to define the volume of > the protein is still a matter of setting your criteria and finding the > right tools to assess these. Not the simplest thing... > > Cheers, > > Tsjerk > > On Mon, May 18, 2009 at 12:22 AM, Justin A. Lemkul > wrote: > > > > > > Chih-Ying Lin wrote: > >> > >> HI > >> How can i know if the protein swell during the MD simulation? > >> > >> What are those indications to "see" the swollen protein? > >> > > > > How do you define the term "swelling?" This again sounds like another > issue > > on defining your own criteria for the expected behavior and reading the > > manual about available analysis tools. > > > > -Justin > > > >> Thank you > >> Lin > >> > >> > >> > >> > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests to the list. Use the www > >> interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > > > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the www > interface > > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Failing installation with --enable-mpi option
I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix="_mpi" it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix="_mpi" checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /bin/sh: /home/sandaka/Desktop/all: No such file or directory configure: WARNING: `missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Am attaching the config.log file herein. I've Openmpi and fftw already installed and in the path.. Couldn't understand what is the error! -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by gromacs configure 4.0.3, which was generated by GNU Autoconf 2.61. Invocation command line was $ ./configure --enable-mpi --disable-nice --program-suffix=_mpi ## - ## ## Platform. ## ## - ## hostname = bhanu.prakash uname -m = i686 uname -r = 2.6.23.1-42.fc8 uname -s = Linux uname -v = #1 SMP Tue Oct 30 13:55:12 EDT 2007 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = i686 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/lib/qt-3.3/bin PATH: /usr/kerberos/bin PATH: /usr/lib/ccache PATH: /usr/local/bin PATH: /usr/bin PATH: /bin PATH: /usr/X11R6/bin PATH: /home/sandaka/bin ## --- ## ## Core tests. ## ## --- ## configure:2087: checking build system type configure:2105: result: i686-pc-linux-gnu configure:2127: checking host system type configure:2142: result: i686-pc-linux-gnu configure:2180: checking for a BSD-compatible install configure:2236: result: /usr/bin/install -c configure:2247: checking whether build environment is sane configure:2290: result: yes configure:2314: WARNING: `missing' script is too old or missing configure:2318: checking for a thread-safe mkdir -p configure:2357: result: /bin/mkdir -p configure:2370: checking for gawk configure:2386: found /usr/bin/gawk configure:2397: result: gawk configure:2408: checking whether make sets $(MAKE) configure:2429: result: yes configure:2612: checking how to create a ustar tar archive configure:2625: tar --version tar (GNU tar) 1.17 Copyright (C) 2007 Free Software Foundation, Inc. License GPLv2+: GNU GPL version 2 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Written by John Gilmore and Jay Fenlason. configure:2628: $? = 0 configure:2668: tardir=conftest.dir && eval tar --format=ustar -chf - "$tardir" >conftest.tar configure:2671: $? = 0 configure:2675: tar -xf - &5 cc (GCC) 4.1.2 20070925 (Red Hat 4.1.2-33) Copyright (
Re: [gmx-users] Failing installation with --enable-mpi option
Thanks Justin, will try your suggestion.. 2009/5/20 Justin A. Lemkul : > > > Bhanu wrote: >> >> I tried to install Gromacs on my Core2Quad pc with the command >> >> ./configure --enable-mpi --disable-nice --program-suffix="_mpi" >> >> it is showing the following error result: >> >> [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice >> --program >> -suffix="_mpi" >> checking build system type... i686-pc-linux-gnu >> checking host system type... i686-pc-linux-gnu >> checking for a BSD-compatible install... /usr/bin/install -c >> checking whether build environment is sane... yes >> /bin/sh: /home/sandaka/Desktop/all: No such file or directory >> configure: WARNING: `missing' script is too old or missing >> checking for a thread-safe mkdir -p... /bin/mkdir -p >> checking for gawk... gawk >> checking whether make sets $(MAKE)... yes >> checking how to create a ustar tar archive... gnutar >> checking for cc... cc >> checking for C compiler default output file name... a.out >> checking whether the C compiler works... yes >> checking whether we are cross compiling... no >> checking for suffix of executables... >> checking for suffix of object files... o >> checking whether we are using the GNU C compiler... yes >> checking whether cc accepts -g... yes >> checking for cc option to accept ISO C89... none needed >> checking for style of include used by make... GNU >> checking dependency style of cc... gcc3 >> checking dependency style of cc... gcc3 >> checking for mpxlc... no >> checking for mpicc... mpicc >> checking whether the MPI cc command works... yes >> checking for catamount... no >> checking how to run the C preprocessor... mpicc -E >> checking whether mpicc accepts -O3... yes >> checking whether mpicc accepts -funroll-all-loops... yes >> checking whether mpicc accepts -O3 -fomit-frame-pointer >> -finline-functions -Wall -Wno-unused -funroll-all-loops... yes >> checking for grep that handles long lines and -e... /bin/grep >> checking for egrep... /bin/grep -E >> checking for ANSI C header files... no >> checking for sys/types.h... yes >> checking for sys/stat.h... yes >> checking for stdlib.h... yes >> checking for string.h... yes >> checking for memory.h... yes >> checking for strings.h... yes >> checking for inttypes.h... yes >> checking for stdint.h... yes >> checking for unistd.h... yes >> checking whether byte ordering is bigendian... no >> checking for int... yes >> checking size of int... configure: error: cannot compute sizeof (int) >> See `config.log' for more details. >> >> Am attaching the config.log file herein. I've Openmpi and fftw already >> installed and in the path.. Couldn't understand what is the error! >> >> > > Have a look at this thread: > > http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html > > -Justin > >> >> >> >> >> >> >> ___ >> gmx-users mailing list gmx-us...@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Failing installation with --enable-mpi option
Dear Justin, could you please write what environmental changes you made to MPICC.. I tried to alter the profile, but it is rejecting all of them.. Bhanu. On 20/05/2009, Bhanu wrote: > Thanks Justin, will try your suggestion.. > > 2009/5/20 Justin A. Lemkul : > > > > > > Bhanu wrote: > >> > >> I tried to install Gromacs on my Core2Quad pc with the command > >> > >> ./configure --enable-mpi --disable-nice --program-suffix="_mpi" > >> > >> it is showing the following error result: > >> > >> [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice > >> --program > >> -suffix="_mpi" > >> checking build system type... i686-pc-linux-gnu > >> checking host system type... i686-pc-linux-gnu > >> checking for a BSD-compatible install... /usr/bin/install -c > >> checking whether build environment is sane... yes > >> /bin/sh: /home/sandaka/Desktop/all: No such file or directory > >> configure: WARNING: `missing' script is too old or missing > >> checking for a thread-safe mkdir -p... /bin/mkdir -p > >> checking for gawk... gawk > >> checking whether make sets $(MAKE)... yes > >> checking how to create a ustar tar archive... gnutar > >> checking for cc... cc > >> checking for C compiler default output file name... a.out > >> checking whether the C compiler works... yes > >> checking whether we are cross compiling... no > >> checking for suffix of executables... > >> checking for suffix of object files... o > >> checking whether we are using the GNU C compiler... yes > >> checking whether cc accepts -g... yes > >> checking for cc option to accept ISO C89... none needed > >> checking for style of include used by make... GNU > >> checking dependency style of cc... gcc3 > >> checking dependency style of cc... gcc3 > >> checking for mpxlc... no > >> checking for mpicc... mpicc > >> checking whether the MPI cc command works... yes > >> checking for catamount... no > >> checking how to run the C preprocessor... mpicc -E > >> checking whether mpicc accepts -O3... yes > >> checking whether mpicc accepts -funroll-all-loops... yes > >> checking whether mpicc accepts -O3 -fomit-frame-pointer > >> -finline-functions -Wall -Wno-unused -funroll-all-loops... yes > >> checking for grep that handles long lines and -e... /bin/grep > >> checking for egrep... /bin/grep -E > >> checking for ANSI C header files... no > >> checking for sys/types.h... yes > >> checking for sys/stat.h... yes > >> checking for stdlib.h... yes > >> checking for string.h... yes > >> checking for memory.h... yes > >> checking for strings.h... yes > >> checking for inttypes.h... yes > >> checking for stdint.h... yes > >> checking for unistd.h... yes > >> checking whether byte ordering is bigendian... no > >> checking for int... yes > >> checking size of int... configure: error: cannot compute sizeof (int) > >> See `config.log' for more details. > >> > >> Am attaching the config.log file herein. I've Openmpi and fftw already > >> installed and in the path.. Couldn't understand what is the error! > >> > >> > > > > Have a look at this thread: > > > > http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html > > > > -Justin > > > >> > >> > >> > >> > >> > >> > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before posting! > >> Please don't post (un)subscribe requests to the list. Use the www > >> interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > > > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > ___ > > gmx-users ma
[gmx-users] Strange error in DNA simulations..
Hi Group, I've tried simulating a five bp dna. It has showed many atoms missing and some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and -mising options. Later editconf_d, genbox_d, and genion_d steps went well. Even grompp_d worked well. But when I issued the run command for mdrun_d, the strange result is coming, repeatedly. I have installed lam-mpi and running gromacs in double precision. The commands I have used are.. pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro neutralized the system with genion_d and grompp_d, mdrun_d with -v and -deffnm commands. Surprisigly, everytime, it is using only two cores of my core2quad processor, delaying the output for all experiments. For this experiment, here is the error report which I donot understand at all! The error report is really frightening to me!!! Here it is! [bh...@localhost doublestrand]$ gedit Testfile [bh...@localhost doublestrand]$ mpirun N C Testfile NNODES=2, MYRANK=1, HOSTNAME=localhost.localdomain NNODES=2, MYRANK=0, HOSTNAME=localhost.localdomain NODEID=1 argc=6 NODEID=0 argc=6 :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.0.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun_d (double precision) (-: Option Filename Type Description -s bhanu.tpr InputRun input file: tpr tpb tpa -o bhanu.trr Output Full precision trajectory: trr trj cpt -x bhanu.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi bhanu.cpt Input, Opt. Checkpoint file -cpo bhanu.cpt Output, Opt. Checkpoint file -c bhanu.gro Output Structure file: gro g96 pdb -e bhanu.edr Output Energy file: edr ene -g bhanu.log Output Log file -dgdl bhanu.xvg Output, Opt. xvgr/xmgr file -fieldbhanu.xvg Output, Opt. xvgr/xmgr file -tablebhanu.xvg Input, Opt. xvgr/xmgr file -tablep bhanu.xvg Input, Opt. xvgr/xmgr file -tableb bhanu.xvg Input, Opt. xvgr/xmgr file -rerunbhanu.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi bhanu.xvg Output, Opt. xvgr/xmgr file -tpid bhanu.xvg Output, Opt. xvgr/xmgr file -ei bhanu.edi Input, Opt. ED sampling input -eo bhanu.edo Output, Opt. ED sampling output -j bhanu.gct Input, Opt. General coupling stuff -jo bhanu.gct Output, Opt. General coupling stuff -ffoutbhanu.xvg Output, Opt. xvgr/xmgr file -devout bhanu.xvg Output, Opt. xvgr/xmgr file -runavbhanu.xvg Output, Opt. xvgr/xmgr file -px bhanu.xvg Output, Opt. xvgr/xmgr file -pf bhanu.xvg Output, Opt. xvgr/xmgr file -mtx bhanu.mtx Output, Opt. Hessian matrix -dn bhanu.ndx Output, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -deffnm string bhanu Set the default filename for all file options -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -[no]sum bool yes Sum the energies at every step -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for
Re: [gmx-users] Strange error in DNA simulations..
On 15/06/2009, Mark Abraham wrote: > > > On 06/15/09, *Bhanu * wrote: > > Hi Group, > I've tried simulating a five bp dna. It has showed many atoms missing and > some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and > -mising options. Later editconf_d, genbox_d, and genion_d steps went well. > Even grompp_d worked well. But when I issued the run command for mdrun_d, > the strange result is coming, repeatedly. I have installed lam-mpi and > running gromacs in double precision. The commands I have used are.. > > pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top > editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro > genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro > > neutralized the system with genion_d and grompp_d, mdrun_d with -v and > -deffnm commands. Surprisigly, everytime, it is using only two cores of my > core2quad processor, delaying the output for all experiments. > > So look up how to configure LAM-MPI to use more. > I am working on that.. but the real confusing thing, is why are DNA simulations failing?? I have no clue.. and requesting for a suggestion! For this experiment, here is the error report which I donot understand at > all! > > The error report is really frightening to me!!! Here it is! > > > See http://oldwiki.gromacs.org/index.php/Errors#Range_Checking_error > > Mark > > ___ > 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 posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ 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 posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange error in DNA simulations..
Hi, I didn't ignore your link, I was trying all things suggested in wiki.. Its the greed for more and more suggestions made me to type those.. Anyway, thanks for the link, buddy! On 15/06/2009, Mark Abraham wrote: > > > > On 06/15/09, *Bhanu * wrote: > > > > On 15/06/2009, Mark Abraham wrote: >> >> >> On 06/15/09, *Bhanu * wrote: >> >> Hi Group, >> I've tried simulating a five bp dna. It has showed many atoms missing and >> some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and >> -mising options. Later editconf_d, genbox_d, and genion_d steps went well. >> Even grompp_d worked well. But when I issued the run command for mdrun_d, >> the strange result is coming, repeatedly. I have installed lam-mpi and >> running gromacs in double precision. The commands I have used are.. >> >> pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top >> editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro >> genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro >> >> neutralized the system with genion_d and grompp_d, mdrun_d with -v and >> -deffnm commands. Surprisigly, everytime, it is using only two cores of my >> core2quad processor, delaying the output for all experiments. >> >> So look up how to configure LAM-MPI to use more. >> > > > I am working on that.. but the real confusing thing, is why are DNA > simulations failing?? I have no clue.. and requesting for a suggestion! > > I gave you a link to content that was likely to explain why your problem > was occurring. If you appear to ignore it, then you won't be likely to get > more :-) > > Mark > > > > >> For this experiment, here is the error report which I donot understand >> at all! >> >> The error report is really frightening to me!!! Here it is! >> >> >> See http://oldwiki.gromacs.org/index.php/Errors#Range_Checking_error >> >> Mark >> >> ___ >> 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 >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Never lose hope on the person you love they maybe the reason your heart > aches today... but they are definitely the reason your heart beats : > COPIED FROM GMAIL CUSTOM MSGS. > > > ___ > 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 posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ 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 posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in dna-protein simulation
Edit your pdb as per ur rtp file / forcefield. On 16/06/2009, Justin A. Lemkul wrote: > > > > nitu sharma wrote: > >> Dear all, >> >>i am trying to simulation of dna-protein complex using >> gromacs with amber port . I am using amber99 port with gromacs-4.0.3 >> version. I am facing problem in running pdb2gmx command .The error comes >> like this- >> --- >> Program pdb2gmx, VERSION 4.0.3 >> Source code file: resall.c, line: 426 >> >> Fatal error: >> Residue 'T' not found in residue topology database >> >> Can anyone suggest me how can I overcome this problem . >> >> > > http://oldwiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database > > -Justin > > Thanks a lot in advance. >> >> Nitu sharma >> Jawaherlal Nehru University >> >> >> >> >> ___ >> 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 >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > 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 posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ 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 posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Protein is moving out of box.
Hi all, am new to Gromacs. I tried a 10 ps simulation with a protein and after the run, the protein came out of the box.. is it good or bad? How can I keep the protein in the box? Waiting for ur reply. Bhanu. -- _ _ (_)(_) (,,) =()= ((__)\ _|L\___/ The Lab Rats ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] protein/dmso simulation
Try "genbox -cp *.gro -ci dmso.gro -p *.top -o *.gro" Gro file for dmso comes built-in with gromacs 3.3. As Justin has directed, forcefields do matter. On 19/08/2008, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > > prasun kumar wrote: > >> dear users >> I am trying to run the simulation fo a protein/DMSO system,Its working >> well till genbox but while running GROMPP I am gettin a fatal error,which is >> atom type 'SD' not found. >> SD is given in the gro & itp file of DMSO. >> what should I do to overcome this problem >> I have tried by replacing SD by S,but its of no use >> I should generate a separate top file for DMSO and then include it in the >> topology file generated for protein >> I tried to do this also using PDB2GMX command but again I am gettin error >> related to 'SD' >> > > Which force field are you using? If you look at the .rtp entry (if > present), it will tell you the correct atomic nomenclature. Otherwise, you > have an inconsistency in the atomtypes definition in your topology. > > -Justin > > please help me.. >> regards &thanx in advance >> >> -- >> PRASUN (ASHOKA) >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> 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 >> > > -- > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > -- _ _ (_)(_) (,,) =()= ((__)\ _|L\___/ The Lab Rats When u r busy judging ppl, you've no time to love'em.. -Nick Vujicic ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Genion failing in parallel runs.
Hi, I'm using Gromacs 3.3.3, installed with double precision. When I run genion with this command: genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral the following error message was generated: Program genion_d Version 3.3.3 sourcecode file: init.c, line 69 Fatal error: run input file prakash.tpr was made for 32 nodes while genion_d expected it to be for 1 node -- System is "protein in water", dodecahedron box. Everything is fine till energy minimisation. genion is failing. Any clue?? Thanks. -- _ _ (_)(_) (,,) =()= ((__)\ _|L\___/ The Lab Rats When u r busy judging ppl, you've no time to love'em.. -Nick Vujicic ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] DSSP and g_sas
Which among DSSP and g_sas is better for calculating solvent accessible surface area of proteins? -- Bhanu Prakash. -- 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 posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DSSP and g_sas
Using DSSP we can also calcuate the surface area, though it doesn't allow changes in probe diameter etc. it does calculate the surface area. I just wish to know whether the performance of DSSP is comparable to g_sas? Should it be used? -- Bhanu Prakash, BARC. > Shalom Bhanu, > > g_sas calculates solvent accessible surface > DSSP find local secondary structure. > > So use g_sas for you calculation. > > Best, > Itamar > > > > On 15/07/10 4:57 PM, Bhanu Prakash Sandaka wrote: >> Which among DSSP and g_sas is better for calculating solvent accessible >> surface area of proteins? > > -- > > > "In theory, there is no difference between theory and practice. But, in > practice, there is." - Jan L.A. van de Snepscheut > > === > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: itamar.k...@monash.edu > > -- 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 posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
