RE: [gmx-users] using rerun to extract energies for protein fromtrr file
Dear Mark, Many thanks for your kind suggestion. I did all sorts of things as you suggested, however still I get the same error. Here are the commands that I use (I used grompp also to generate different tpr files): $ tpbconv -s fullmd.tpr -n index.ndx -o tpxout.tpr $ trjconv -f md_traj.trr -n index.ndx -s tpxout.tpr -o trajout.trr $ mdrun_d -s tpxout.tpr -o md_prot_final.trr -c md_prot_final.gro -e md_prot.edr -g md_prot.log -rerun trajout.trr I am a bit confused and don't know what I am doing wrong. Is there any way to extract coordinates of just protein molecule for different frames and then calculate their energies (this is just a guess)? Cheers, Siavoush From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 2009/01/12 03:47 ب.ظ To: Discussion list for GROMACS users Subject: Re: [gmx-users] using rerun to extract energies for protein fromtrr file Siavoush Dastmalchi wrote: Dear list, I am trying to extract energy profile for a protein molecule using rerun program from trajectory obtained by MD of protein solvated in a water box. I have created index file and reedited the original mdp file (removed the SOLs from it) to get a new tpr file using grompp. I have extracted a coordinate file and also generated top file for this coordinate file. When I run the mdrun using -rerun option, it fails and gives the following error message: tpbconv allows you to create subsets of .tpr files, so you should also use trjconv to make a matching subset from your .trr files and then use mdrun -rerun. ** Program mdrun_d, VERSION 3.3.1 Source code file: clincs.c, line: 559 Fatal error: Too many LINCS warnings (11741) - aborting to avoid logfile runaway. This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations. If you know what you are doing you can adjust the lincs warning threshold in your mdp file, but normally it is better to fix the problem. ** This does not look like you are doing a rerun. LINCS should not be invoked, IMO. Mark ___ 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 winmail.dat___ 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] low latency
On Jan 13, 2009, at 9:15 PM, ha salem wrote: Dear Karsten and gromacs specialists I enabled flow control on hp procurve now I want to know how I can config low latency on the network ?is it required? thank you There are quite some parameters that affect Ethernet performance. They can be found in the /proc/net/ filesystem, where exactly will depend on your type of system. These settings can also be changed with programs like e.g. ethtool. Did your performance get better with flow control? I would not look at the CPU usage % but perform a benchmark on 1, 2, 4, ... CPUs and compare the ns/day numbers before and after you make changes. These numbers are far more reliable because a high CPU usage % does not necessarily mean you have good scaling. You could also compare the md.log files to find out which parts of mdrun eat up most of the time. Carsten ___ 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] using rerun to extract energies for protein fromtrr file
Siavoush Dastmalchi wrote: Dear Mark, Many thanks for your kind suggestion. I did all sorts of things as you suggested, however still I get the same error. Here are the commands that I use (I used grompp also to generate different tpr files): $ tpbconv -s fullmd.tpr -n index.ndx -o tpxout.tpr $ trjconv -f md_traj.trr -n index.ndx -s tpxout.tpr -o trajout.trr $ mdrun_d -s tpxout.tpr -o md_prot_final.trr -c md_prot_final.gro -e md_prot.edr -g md_prot.log -rerun trajout.trr I am a bit confused and don't know what I am doing wrong. Is there any way to extract coordinates of just protein molecule for different frames and then calculate their energies (this is just a guess)? Select just the protein group from the index file when using the *conv utilities? (I haven't actually ever done this procedure, but that's about how it should work) Mark ___ 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] Extract diagonal from xpm matrix
Hello, Is there any way to extract the diagnonal from an xpm matrix ? What I am trying to do, is to calculate the RMSD between two trajectories using g_rms: g_rms -s topol.tpr -f traj1.xtc -f2 traj2.xtc -m rmsd.xpm and the RMSD at the same time points is supposed to be the diagonal of the rmsd.xpm matrix. Maybe there is another way to do it. Many thanks Andreas ___ 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] g_rotacf, order parameter S2 problem
On Sun, 11 Jan 2009 12:50:00 +0800 Dechang Li li.d...@gmail.com wrote: Dear all, I used g_rotacf to calculate the order parameter (S2, N-H bond in main chian). Thanks to Xavier Periole's advice, I make the index file and obtained some results. However, some results I got made me puzzling that the order parameter is negative! Here is one of my results: @title Rotational Correlation Function @xaxis label Time (ps) @yaxis label C(t) @TYPE xy ... 119944.000-0.16902 119946.000-0.16845 119948.000-0.16812 119950.000-0.16845 119952.000-0.16834 119954.000-0.16825 119956.000-0.16875 119958.000-0.16823 119960.000-0.16850 119962.000-0.16885 119964.000-0.16892 119966.000-0.16924 119968.000-0.16885 119970.000-0.16928 119972.000-0.16889 119974.000-0.16901 119976.000-0.16866 119978.000-0.16901 119980.000-0.16895 119982.000-0.16953 119984.000-0.16932 119986.000-0.16961 119988.000-0.16947 119990.000-0.16890 119992.000-0.16952 119994.000-0.16986 119996.000-0.16970 119998.000-0.16941 12.000-0.16908 The command I used is : g_rotacf -s Order.tpr -f Order.trr -d -n index.ndx -P 2 -nice 0 . Actually, when I used the option -P 1, the negative results appear similarly. Before I calculated the S2 parameter, I removed the rotation and translation movement of the molecule using the tool trjconv. Is that the negative results reasonable? No! the order parameter must be between 0 and 1. Considering the length of your simulation (120 ns) most of the NH vectors will have sampled enough for you to get a reasonable value. However some of them will not and it also depends on the topology of your protein. You should look at the curve and try to make sense with its shape. Undulations are typical of lack of convergence. Note that in some cases it is very difficult to obtain a smooth curve. Eg. we had to run ~1000 cases and average them to get a acceptable curve. You do not need to do that but be aware that it is not always trivial to get a C(t) converged. Anyways, a negative value without undulations would indicate that you did something wrong somewhere. May be in the fitting procedure. XAvier. Best regards, 2009-1-11 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn = ___ 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 - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ 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: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
Hi, We have for now concluded that this is probably an issue related to lam7.1.4. There were a few other users with mdrun crashes/hangs. What it the status of your problems? Berk Date: Tue, 13 Jan 2009 13:02:47 +0100 From: patrick.fu...@univ-paris-diderot.fr To: gmx-users@gromacs.org Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Hi Berk, it hangs after approximatively 45000 steps (the system is a simple DLPC bilayer), and there was a cpt file that has been generated (but it was generated [09:48] before it started to hang [9:58]) : - [fu...@cumin 2]$ ls -ltrh [snip] -rw-r--r-- 1 fuchs dsimb 384K janv. 13 09:33 traj.trr -rw-r--r-- 1 fuchs dsimb 385K janv. 13 09:48 state.cpt -rw-r--r-- 1 fuchs dsimb 66K janv. 13 09:57 md.log -rw-r--r-- 1 fuchs dsimb 5,4M janv. 13 09:58 traj.xtc -rw-r--r-- 1 fuchs dsimb 92K janv. 13 09:58 ener.edr [fu...@cumin 2]$ date Tue Jan 13 10:16:22 CET 2009 - The version of MPI is: LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University. So shall I send you the tpr and cpt files off list ? Ciao, Patrick Berk Hess a écrit : Hi, This is strange. You run on 4 nodes and all processes hang at the same MPI call. I see no reason why they should hang if they are all at the correct call. After how many steps does this happen? If it is not much I can try to see if it also hangs on our system. Otherwise, could you try to generate a checkpoint file with which it hangs quickly? What version of MPI are you using? Berk Date: Tue, 13 Jan 2009 10:53:25 +0100 From: patrick.fu...@univ-paris-diderot.fr To: gmx-users@gromacs.org Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Hi Berk, I did a test on gromacs-4.0.2 under Fedora 10 (with fftw-3.0.1 and lam-7.1.4), using a slightly upgraded version of gcc compared to my previous post (gcc version 4.3.2 20081105 (Red hat 4.3.2-7)) on the same hardware but it still hangs (so both FC9 and FC10 give the same problem, while FC8 does not). Finally I could test mdrun_mpi in the debugger and here are the results of my tests. You were right, it seems that mdrun hangs at an MPI call, here are the outputs of each xterm: XTERM1 === GNU gdb Fedora (6.8-29.fc10) Copyright (C) 2008 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 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. Type show copying and show warranty for details. This GDB was configured as x86_64-redhat-linux-gnu... (gdb) run Starting program: /usr/local/gromacs-4.0.2/bin/mdrun_mpi [Thread debugging using libthread_db enabled] [New Thread 0x12df30 (LWP 8285)] NNODES=4, MYRANK=0, HOSTNAME=cumin.dsimb.inserm.fr NODEID=0 argc=1 :-) G R O M A C S (-: Giant Rising Ordinary Mutants for A Clerical Setup :-) VERSION 4.0.2 (-: [snip] starting mdrun 'Pure DLPC bilayer with 128 lipids and 3655 SPC water' 500 steps, 1.0 ps. ^C Program received signal SIGINT, Interrupt. 0x003b978cc087 in sched_yield () from /lib64/libc.so.6 Missing separate debuginfos, use: debuginfo-install e2fsprogs-libs-1.41.3-2.fc10.x86_64 glibc-2.9-3.x86_64 libICE-1.0.4-4.fc10.x86_64 libSM-1.1.0-2.fc10.x86_64 libX11-1.1.4-6.fc10.x86_64 libXau-1.0.4-1.fc10.x86_64 libXdmcp-1.0.2-6.fc10.x86_64 libxcb-1.1.91-5.fc10.x86_64 (gdb) where #0 0x003b978cc087 in sched_yield () from /lib64/libc.so.6 #1 0x00770c83 in lam_ssi_rpi_usysv_proc_read_env () #2 0x00784a39 in lam_ssi_rpi_usysv_advance_common () #3 0x0074a1e0 in _mpi_req_advance () #4 0x0073ced0 in lam_send () #5 0x0075328e in MPI_Send () #6 0x0074d7ec in MPI_Sendrecv () #7 0x004aebfd in gmx_sum_qgrid_dd () #8 0x004b40bb in gmx_pme_do () #9 0x00479a58 in do_force_lowlevel () #10 0x004d1d32 in do_force () #11 0x004214d2 in do_md () #12 0x0041bea0 in mdrunner () #13 0x00422b94 in main () (gdb) === XTERM2 === GNU gdb Fedora (6.8-29.fc10) Copyright (C) 2008 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 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. Type show copying and show warranty for details. This GDB was configured as x86_64-redhat-linux-gnu... (gdb) run Starting program: /usr/local/gromacs-4.0.2/bin/mdrun_mpi [Thread
RE: [gmx-users] g_rotacf, order parameter S2 problem
Hi, I would say rotational acf's can be negative. In most cases this will indicate bad sampling. This is not suprising considering the extremely long times you printed. I guess you get positive values for shorter correlation times. Berk From: x.peri...@rug.nl Subject: Re: [gmx-users] g_rotacf, order parameter S2 problem To: gmx-users@gromacs.org Date: Wed, 14 Jan 2009 12:23:11 +0100 On Sun, 11 Jan 2009 12:50:00 +0800 Dechang Li li.d...@gmail.com wrote: Dear all, I used g_rotacf to calculate the order parameter (S2, N-H bond in main chian). Thanks to Xavier Periole's advice, I make the index file and obtained some results. However, some results I got made me puzzling that the order parameter is negative! Here is one of my results: @title Rotational Correlation Function @xaxis label Time (ps) @yaxis label C(t) @TYPE xy ... 119944.000-0.16902 119946.000-0.16845 119948.000-0.16812 119950.000-0.16845 119952.000-0.16834 119954.000-0.16825 119956.000-0.16875 119958.000-0.16823 119960.000-0.16850 119962.000-0.16885 119964.000-0.16892 119966.000-0.16924 119968.000-0.16885 119970.000-0.16928 119972.000-0.16889 119974.000-0.16901 119976.000-0.16866 119978.000-0.16901 119980.000-0.16895 119982.000-0.16953 119984.000-0.16932 119986.000-0.16961 119988.000-0.16947 119990.000-0.16890 119992.000-0.16952 119994.000-0.16986 119996.000-0.16970 119998.000-0.16941 12.000-0.16908 The command I used is : g_rotacf -s Order.tpr -f Order.trr -d -n index.ndx -P 2 -nice 0 . Actually, when I used the option -P 1, the negative results appear similarly. Before I calculated the S2 parameter, I removed the rotation and translation movement of the molecule using the tool trjconv. Is that the negative results reasonable? No! the order parameter must be between 0 and 1. Considering the length of your simulation (120 ns) most of the NH vectors will have sampled enough for you to get a reasonable value. However some of them will not and it also depends on the topology of your protein. You should look at the curve and try to make sense with its shape. Undulations are typical of lack of convergence. Note that in some cases it is very difficult to obtain a smooth curve. Eg. we had to run ~1000 cases and average them to get a acceptable curve. You do not need to do that but be aware that it is not always trivial to get a C(t) converged. Anyways, a negative value without undulations would indicate that you did something wrong somewhere. May be in the fitting procedure. XAvier. Best regards, 2009-1-11 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn = ___ 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 - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ 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 _ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx___ 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] using rerun to extract energies for protein fromtrrfile
Hi there, That is what I do. I select just protein group. Siavoush From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Wed 2009/01/14 02:20 ب.ظ To: Discussion list for GROMACS users Subject: Re: [gmx-users] using rerun to extract energies for protein fromtrrfile Siavoush Dastmalchi wrote: Dear Mark, Many thanks for your kind suggestion. I did all sorts of things as you suggested, however still I get the same error. Here are the commands that I use (I used grompp also to generate different tpr files): $ tpbconv -s fullmd.tpr -n index.ndx -o tpxout.tpr $ trjconv -f md_traj.trr -n index.ndx -s tpxout.tpr -o trajout.trr $ mdrun_d -s tpxout.tpr -o md_prot_final.trr -c md_prot_final.gro -e md_prot.edr -g md_prot.log -rerun trajout.trr I am a bit confused and don't know what I am doing wrong. Is there any way to extract coordinates of just protein molecule for different frames and then calculate their energies (this is just a guess)? Select just the protein group from the index file when using the *conv utilities? (I haven't actually ever done this procedure, but that's about how it should work) Mark ___ 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 winmail.dat___ 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: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
On Wed, 2009-01-14 at 12:27 +0100, Berk Hess wrote: Hi, We have for now concluded that this is probably an issue related to lam7.1.4. There were a few other users with mdrun crashes/hangs. What it the status of your problems? You can try with the version in Fedora, which is debuggable and compiled against OpenMPI. # yum -y install gromacs gromacs-mpi All binaries have been renamed to start with g_, e.g. g_grompp, g_mdrun and so on. Suffixes: g_mdrun single precision version g_mdrun_d double precision version g_mdrun_mpi single precision, MPI version g_mdrun_mpi_d double precision, MPI version PS. Could somebody please add the Fedora specifics to the installation part of the webpage? At least switching to new SRPMS would be good. Feel free to use my spec and include it in the GROMACS source distribution. SPEC: https://cvs.fedoraproject.org/viewvc/devel/gromacs/gromacs.spec?view=log -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ 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] atom H is missing in the first residue in a chain
Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option -missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c- terminus? How can I fix this? Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE ___ 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] atom H is missing in the first residue in a chain
Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option -missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] atom H is missing in the first residue in a chain
hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option -missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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] atom H is missing in the first residue in a chain
What is your exact pdb2gmx command line? -Justin Zhong Zheng wrote: hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option -missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] atom H is missing in the first residue in a chain
Zhong Zheng wrote: I tried this: pdb2gmx -f prot.pdb -ignh, not working What I am using is : pdb2gmx -f prot.pdb -missing Does the behavior occur when you process each chain separately? Which force field are you using? Which version of Gromacs are you using, and how was it compiled? I experienced the same behavior in version 3.3.1, resulting from a broken Ubuntu package. -Justin On Jan 14, 2009, at 2:16 PM, Justin A. Lemkul wrote: What is your exact pdb2gmx command line? -Justin Zhong Zheng wrote: hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option -missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] atom H is missing in the first residue in a chain
Please keep all correspondence on the list. Zhong Zheng wrote: Yes. Amber. Gromacs Version 4.0.2. It's compiled on my computer, macbook. I followed standard procedure,nothing special. The Amber force fields use their own special nomenclature, so N-terminal alanine would actually be called NALA. You will have to modify your .pdb file to correspond with Amber naming conventions before this step will complete properly. -Justin On Jan 14, 2009, at 2:28 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: I tried this: pdb2gmx -f prot.pdb -ignh, not working What I am using is : pdb2gmx -f prot.pdb -missing Does the behavior occur when you process each chain separately? Which force field are you using? Which version of Gromacs are you using, and how was it compiled? I experienced the same behavior in version 3.3.1, resulting from a broken Ubuntu package. -Justin On Jan 14, 2009, at 2:16 PM, Justin A. Lemkul wrote: What is your exact pdb2gmx command line? -Justin Zhong Zheng wrote: hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option -missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. 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 list
Re: [gmx-users] atom H is missing in the first residue in a chain
Zhong Zheng wrote: You mean rename ALA as NALA in the .pdb for the n-terminus Ala? If so, i tried already and still not working. Yes, you would have to rename all N-terminal ALA as NALA, as well as specify the correct Amber residue names for all other amino acids in your structure (i.e., C-terminal residues, histidines, etc). An easy way might be to process your .pdb with xLeap (now free as part of AmberTools), and use the output .pdb as your input into pdb2gmx. Have you carefully followed all instructions here: http://chemistry.csulb.edu/ffamber/#usage Have you updated your aminoacids.dat appropriately (see above link)? -Justin On Jan 14, 2009, at 2:38 PM, Justin A. Lemkul wrote: Please keep all correspondence on the list. Zhong Zheng wrote: Yes. Amber. Gromacs Version 4.0.2. It's compiled on my computer, macbook. I followed standard procedure,nothing special. The Amber force fields use their own special nomenclature, so N-terminal alanine would actually be called NALA. You will have to modify your .pdb file to correspond with Amber naming conventions before this step will complete properly. -Justin On Jan 14, 2009, at 2:28 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: I tried this: pdb2gmx -f prot.pdb -ignh, not working What I am using is : pdb2gmx -f prot.pdb -missing Does the behavior occur when you process each chain separately? Which force field are you using? Which version of Gromacs are you using, and how was it compiled? I experienced the same behavior in version 3.3.1, resulting from a broken Ubuntu package. -Justin On Jan 14, 2009, at 2:16 PM, Justin A. Lemkul wrote: What is your exact pdb2gmx command line? -Justin Zhong Zheng wrote: hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option -missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 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 gmx-users-requ...@gromacs.org. 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 list
Re: [gmx-users] atom H is missing in the first residue in a chain
You mean rename ALA as NALA in the .pdb for the n-terminus Ala? If so, i tried already and still not working. On Jan 14, 2009, at 2:38 PM, Justin A. Lemkul wrote: Please keep all correspondence on the list. Zhong Zheng wrote: Yes. Amber. Gromacs Version 4.0.2. It's compiled on my computer, macbook. I followed standard procedure,nothing special. The Amber force fields use their own special nomenclature, so N- terminal alanine would actually be called NALA. You will have to modify your .pdb file to correspond with Amber naming conventions before this step will complete properly. -Justin On Jan 14, 2009, at 2:28 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: I tried this: pdb2gmx -f prot.pdb -ignh, not working What I am using is : pdb2gmx -f prot.pdb -missing Does the behavior occur when you process each chain separately? Which force field are you using? Which version of Gromacs are you using, and how was it compiled? I experienced the same behavior in version 3.3.1, resulting from a broken Ubuntu package. -Justin On Jan 14, 2009, at 2:16 PM, Justin A. Lemkul wrote: What is your exact pdb2gmx command line? -Justin Zhong Zheng wrote: hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option - missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. 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)
[gmx-users] How does MDrun number atoms?
Our minimization ended with a large net force on atom 0. Since there is no atom 0 in our .gro, .top, or .ndx files, is mdrun re-numbering the atoms in our system according to some scheme, or is this an indication that something very wrong is happening? -Travis Trudeau, MSc. student at University of Victoria ___ 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] How does MDrun number atoms?
ttrudeau wrote: Our minimization ended with a large net force on atom 0. Since there is no atom 0 in our .gro, .top, or .ndx files, is mdrun re-numbering the atoms in our system according to some scheme, or is this an indication that something very wrong is happening? Numbering in the .tpr starts from 0 (do a gmxdump to see for yourself). -Justin -Travis Trudeau, MSc. student at University of Victoria ___ 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 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to treat an isolated iron (Fe 2+)
hi all I have an isolated iron in the protein. If I don't' put that iron in, everything runs through fine. However, if I put the iron in, the mdrun step (doing energy minimization) will clash. It says segmentation fault and lots of LINCS WARNING. The iron has a +2 charge with four His ligands and one Glu ligand. The total charge for the complex should be +1. Is there a good way to treat this isolated iron? Thanks a lot. Zhong Zheng ___ 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] atom H is missing in the first residue in a chain
Thanks Justin. I fixed it this time. I basically renamed the terminal residues. The reason it didn't work last time is probably because some format problem. Thanks again. On Jan 14, 2009, at 2:50 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: You mean rename ALA as NALA in the .pdb for the n-terminus Ala? If so, i tried already and still not working. Yes, you would have to rename all N-terminal ALA as NALA, as well as specify the correct Amber residue names for all other amino acids in your structure (i.e., C-terminal residues, histidines, etc). An easy way might be to process your .pdb with xLeap (now free as part of AmberTools), and use the output .pdb as your input into pdb2gmx. Have you carefully followed all instructions here: http://chemistry.csulb.edu/ffamber/#usage Have you updated your aminoacids.dat appropriately (see above link)? -Justin On Jan 14, 2009, at 2:38 PM, Justin A. Lemkul wrote: Please keep all correspondence on the list. Zhong Zheng wrote: Yes. Amber. Gromacs Version 4.0.2. It's compiled on my computer, macbook. I followed standard procedure,nothing special. The Amber force fields use their own special nomenclature, so N- terminal alanine would actually be called NALA. You will have to modify your .pdb file to correspond with Amber naming conventions before this step will complete properly. -Justin On Jan 14, 2009, at 2:28 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: I tried this: pdb2gmx -f prot.pdb -ignh, not working What I am using is : pdb2gmx -f prot.pdb -missing Does the behavior occur when you process each chain separately? Which force field are you using? Which version of Gromacs are you using, and how was it compiled? I experienced the same behavior in version 3.3.1, resulting from a broken Ubuntu package. -Justin On Jan 14, 2009, at 2:16 PM, Justin A. Lemkul wrote: What is your exact pdb2gmx command line? -Justin Zhong Zheng wrote: hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option - missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/ MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/ users.php -- Justin A. Lemkul Graduate Research Assistant
Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
Hi all, finally we (Berk and I) could find that there is a problem with lam-7.1.4 under Fedora9/Fedora10. Initially I thought it affected only gromacs-4 but a PhD student of my lab reported identical problems with gromacs-3.3 (hanging problems), while under FC8 I had no problem at all with the same hardware. So if you want to run gromacs-4 (or any version) under FC9/FC10, the fix I tested and that works is to use openmpi as an alternative to lam-7.1.4 (I only tested the last version openmpi-1.2.8). I didn't test other versions of lam (7.0.?) but it seems that the developers advice to switch to openmpi. So for the two other users (Bernhard and Antoine) who reported identical problems to the mailing list (see http://www.gromacs.org/pipermail/gmx-users/2008-December/038594.html and http://www.gromacs.org/pipermail/gmx-users/2008-December/038623.html) can you please check out that it works on your hardware using openmpi? Hope it helps, Patrick Berk Hess a écrit : Hi, We have for now concluded that this is probably an issue related to lam7.1.4. There were a few other users with mdrun crashes/hangs. What it the status of your problems? Berk Date: Tue, 13 Jan 2009 13:02:47 +0100 From: patrick.fu...@univ-paris-diderot.fr To: gmx-users@gromacs.org Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Hi Berk, it hangs after approximatively 45000 steps (the system is a simple DLPC bilayer), and there was a cpt file that has been generated (but it was generated [09:48] before it started to hang [9:58]) : - [fu...@cumin 2]$ ls -ltrh [snip] -rw-r--r-- 1 fuchs dsimb 384K janv. 13 09:33 traj.trr -rw-r--r-- 1 fuchs dsimb 385K janv. 13 09:48 state.cpt -rw-r--r-- 1 fuchs dsimb 66K janv. 13 09:57 md.log -rw-r--r-- 1 fuchs dsimb 5,4M janv. 13 09:58 traj.xtc -rw-r--r-- 1 fuchs dsimb 92K janv. 13 09:58 ener.edr [fu...@cumin 2]$ date Tue Jan 13 10:16:22 CET 2009 - The version of MPI is: LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University. So shall I send you the tpr and cpt files off list ? Ciao, Patrick Berk Hess a écrit : Hi, This is strange. You run on 4 nodes and all processes hang at the same MPI call. I see no reason why they should hang if they are all at the correct call. After how many steps does this happen? If it is not much I can try to see if it also hangs on our system. Otherwise, could you try to generate a checkpoint file with which it hangs quickly? What version of MPI are you using? Berk Date: Tue, 13 Jan 2009 10:53:25 +0100 From: patrick.fu...@univ-paris-diderot.fr To: gmx-users@gromacs.org Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Hi Berk, I did a test on gromacs-4.0.2 under Fedora 10 (with fftw-3.0.1 and lam-7.1.4), using a slightly upgraded version of gcc compared to my previous post (gcc version 4.3.2 20081105 (Red hat 4.3.2-7)) on the same hardware but it still hangs (so both FC9 and FC10 give the same problem, while FC8 does not). Finally I could test mdrun_mpi in the debugger and here are the results of my tests. You were right, it seems that mdrun hangs at an MPI call, here are the outputs of each xterm: XTERM1 === GNU gdb Fedora (6.8-29.fc10) Copyright (C) 2008 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 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. Type show copying and show warranty for details. This GDB was configured as x86_64-redhat-linux-gnu... (gdb) run Starting program: /usr/local/gromacs-4.0.2/bin/mdrun_mpi [Thread debugging using libthread_db enabled] [New Thread 0x12df30 (LWP 8285)] NNODES=4, MYRANK=0, HOSTNAME=cumin.dsimb.inserm.fr NODEID=0 argc=1 :-) G R O M A C S (-: Giant Rising Ordinary Mutants for A Clerical Setup :-) VERSION 4.0.2 (-: [snip] starting mdrun 'Pure DLPC bilayer with 128 lipids and 3655 SPC water' 500 steps, 1.0 ps. ^C Program received signal SIGINT, Interrupt. 0x003b978cc087 in sched_yield () from /lib64/libc.so.6 Missing separate debuginfos, use: debuginfo-install e2fsprogs-libs-1.41.3-2.fc10.x86_64 glibc-2.9-3.x86_64 libICE-1.0.4-4.fc10.x86_64 libSM-1.1.0-2.fc10.x86_64 libX11-1.1.4-6.fc10.x86_64 libXau-1.0.4-1.fc10.x86_64 libXdmcp-1.0.2-6.fc10.x86_64 libxcb-1.1.91-5.fc10.x86_64 (gdb) where #0 0x003b978cc087 in sched_yield () from /lib64/libc.so.6 #1 0x00770c83 in lam_ssi_rpi_usysv_proc_read_env () #2 0x00784a39 in lam_ssi_rpi_usysv_advance_common () #3 0x0074a1e0 in _mpi_req_advance () #4 0x0073ced0 in lam_send () #5 0x0075328e in
Re: [gmx-users] atom H is missing in the first residue in a chain
Hi Justin/Zhong Zheng, Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. It's actually almost opposite: -ignh ignores all hydrogens present, thus stripping them from the .pdb file. The relevant ones are then added back from the .hdb database. When you don't use -ignh pdb2gmx expects all hydrogens in the .pdb file to correspond to atoms listed for a residue in the .rtp file. If a hydrogen is not present it will be rebuilt anyway, otherwise the position given will be used. The use of -ignh is when you have hydrogen atoms listed that are not in the force field description, like in an NMR file, processed for a united atom force field. Crystal structures will usually process well without -ignh, since no hydrogens are present to ignore in the first place :) Cheers, Tsjerk -- 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
