Re: [gmx-users] error in umbrella sampling tutorial
http://lmgtfy.com/?q=There+is+a+dangling+bond+at+at+least+one+of+the+terminal+ends.+Fix+your+coordinate+file%2C+add+a+new+terminal+database+entry+(.tdb)%2C+or+select+the+proper+existing+terminal+entry . On Thu, Apr 23, 2015 at 8:47 AM, Ayesha Fatima ayeshafatima...@gmail.com wrote: Dear Justin, I am learning to use the steered dynamics method implemented in gromacs. somehow your website is not accessible today so i cannot download the modified files of the fibrils for simulation. so i started withe the original file 2BEG.pdb and if i dont select the N and C termini modifications i get the error ... There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. . Could you guide me through the issue? Thank you Regards Ayesha Fatima PhD candidate, UM, Malaysia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] MD run failed..
Exactly. The reason I asked On Fri, Feb 20, 2015 at 1:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/20/15 1:01 PM, HANNIBAL LECTER wrote: Just out of curiosity what does -0.1 actually mean? It means someone made a mistake :) It's not physically sensible. tau-t should be a positive decimal or -1 to turn off coupling for that group. Using -0.1 doesn't make any sense. It's probably the primary reason for failure here. -Justin On Fri, Feb 20, 2015 at 8:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/20/15 6:51 AM, Kalyanashis Jana wrote: Dear all, I am doing an MD simulation of a protein system. Energy minimization step has been completed smoothly but the position restraint MD run is not running properly(after 500-900 steps have been stopped automatically). Even it has not shown any error or anything. I have used a drug molecule in the cavity of the active site. When the box size was 10 X 12 X 25, it was run only 100 steps and with 15 X 15 X 28 box size it was run 500-900 steps. I could not understand what is the problem. Can anyone please help me? The pr.mdp file is cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 100 ; total 1000.0 ps. nstcomm = 100 nstxout = 250 ; ouput coordinates every 0.5 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 100 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; V-rescale temparature coupling is on Tcoupl= V-rescale tau_t = 1.01.0-0.1 1.0 1.0 tc_grps = SOLNA protein DRG CL ref_t = 300300300 300 300 This thermostat setup is nonsensical. http://www.gromacs.org/Documentation/Terminology/ Thermostats#What_Not_To_Do -Justin ; Pressure coupling is on pcoupl = berendsen ; Use Parrinello-Rahman for research work pcoupltype = isotropic ; Use semiisotropic when working with membranes tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord-scaling= all ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thanks in advance, Kalyanashis Jana. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] MD run failed..
Just out of curiosity what does -0.1 actually mean? On Fri, Feb 20, 2015 at 8:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/20/15 6:51 AM, Kalyanashis Jana wrote: Dear all, I am doing an MD simulation of a protein system. Energy minimization step has been completed smoothly but the position restraint MD run is not running properly(after 500-900 steps have been stopped automatically). Even it has not shown any error or anything. I have used a drug molecule in the cavity of the active site. When the box size was 10 X 12 X 25, it was run only 100 steps and with 15 X 15 X 28 box size it was run 500-900 steps. I could not understand what is the problem. Can anyone please help me? The pr.mdp file is cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 100 ; total 1000.0 ps. nstcomm = 100 nstxout = 250 ; ouput coordinates every 0.5 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 100 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; V-rescale temparature coupling is on Tcoupl= V-rescale tau_t = 1.01.0-0.1 1.0 1.0 tc_grps = SOLNA protein DRG CL ref_t = 300300300 300 300 This thermostat setup is nonsensical. http://www.gromacs.org/Documentation/Terminology/ Thermostats#What_Not_To_Do -Justin ; Pressure coupling is on pcoupl = berendsen ; Use Parrinello-Rahman for research work pcoupltype = isotropic ; Use semiisotropic when working with membranes tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord-scaling= all ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thanks in advance, Kalyanashis Jana. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding DSSP
Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is not a scope to specify using the -ver command in this particular version as opposed to the newer versions (5.0.4). By '' I meant do_dssp -f prot.xtc -s prot.tpr. How do I specify a dssp version in gromacs-4.5.6? Secondly, I did install Gromacs-5.0.4 for comparison, and I am using DSSP 2.0.4 again. This time I am using do_dssp -f prot.xtc -s prot.tpr -ver 2 The output I am getting is shown below. Not sure what is going on. *There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp -i ddJszHtZ -o ddRZ5pwg /dev/null 2 /dev/null'Reading frame 0 time 0.000 Back Off! I just backed up ddJszHtZ to ./#ddJszHtZ.1#---Program do_dssp, VERSION 5.0.4Source code file: /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670Fatal error:Failed to execute command: Try specifying your dssp version with the -ver option.For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors---* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding DSSP
Thanks for your reply. Couple of things. I don't really know where to get older dssp binaries. I couldn't find them available for download in the dssp website. I renamed the mkdssp binary to dssp so I am sure nothing is wrong out there when I export the binaries for utilization in gromacs. On Feb 16, 2015 3:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 3:15 PM, HANNIBAL LECTER wrote: Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is not a scope to specify using the -ver command in this particular version as opposed to the newer versions (5.0.4). By '' I meant do_dssp -f prot.xtc -s prot.tpr. How do I specify a dssp version in gromacs-4.5.6? I forget when the -ver flag was introduced. Safe bet is if you're using an ancient GROMACS version, you need a similarly ancient DSSP (version 1.0.x). Secondly, I did install Gromacs-5.0.4 for comparison, and I am using DSSP 2.0.4 again. This time I am using do_dssp -f prot.xtc -s prot.tpr -ver 2 The output I am getting is shown below. Not sure what is going on. *There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp -i ddJszHtZ -o ddRZ5pwg /dev/null 2 /dev/null'Reading frame 0 time My guess is that mkdssp is not actually the same thing as dssp - make sure you've installed a real, functional dssp binary. -Justin 0.000 Back Off! I just backed up ddJszHtZ to ./#ddJszHtZ.1#-- -Program do_dssp, VERSION 5.0.4Source code file: /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670Fatal error:Failed to execute command: Try specifying your dssp version with the -ver option.For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors- --* -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding DSSP
Okay, so the same errors seem to be persisting. I am not sure what can possibly go wrong in this case. The dssp program seems to be working (just typing dssp in the shell gives information regarding the versions of dssp that has been used). The dsspold program doesn't seem to be doing much. Does anyone know of a version of DSSP executable corresponding to a working Gromacs version? On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 4:07 PM, HANNIBAL LECTER wrote: Thanks for your reply. Couple of things. I don't really know where to get older dssp binaries. I couldn't find them available for download in the dssp website. http://swift.cmbi.ru.nl/gv/dssp/ Click on Distributions and at the bottom of that page, DSSPold is the old version. I renamed the mkdssp binary to dssp so I am sure nothing is wrong out there when I export the binaries for utilization in gromacs. Aside from the usual advice of making sure the binary is actually executable (and actually runs, check with ./dssp -V for instance), there's little to go on here. -Justin On Feb 16, 2015 3:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 3:15 PM, HANNIBAL LECTER wrote: Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is not a scope to specify using the -ver command in this particular version as opposed to the newer versions (5.0.4). By '' I meant do_dssp -f prot.xtc -s prot.tpr. How do I specify a dssp version in gromacs-4.5.6? I forget when the -ver flag was introduced. Safe bet is if you're using an ancient GROMACS version, you need a similarly ancient DSSP (version 1.0.x). Secondly, I did install Gromacs-5.0.4 for comparison, and I am using DSSP 2.0.4 again. This time I am using do_dssp -f prot.xtc -s prot.tpr -ver 2 The output I am getting is shown below. Not sure what is going on. *There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp -i ddJszHtZ -o ddRZ5pwg /dev/null 2 /dev/null'Reading frame 0 time My guess is that mkdssp is not actually the same thing as dssp - make sure you've installed a real, functional dssp binary. -Justin 0.000 Back Off! I just backed up ddJszHtZ to ./#ddJszHtZ.1#-- -Program do_dssp, VERSION 5.0.4Source code file: /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670Fatal error:Failed to execute command: Try specifying your dssp version with the -ver option.For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors- --* -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding DSSP
Sorry, yes, I actually made a copy and pasted in the /usr/bin directory as well. So there IS actually a copy of the same program. Yes, my system is 64 bit. Just as a test case, I tried with the 32-bit version as well. Same error as above. On Mon, Feb 16, 2015 at 6:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 6:40 PM, HANNIBAL LECTER wrote: Okay. what can be possibly wrong? I mean if someone CAN run Gromacs-5.0.4 + DSSP 2.0.4, it should be running in other systems as well unless I am messing something up. So I list my steps. 1. Download the executable from ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source code, but just the binaries). 2. rename the file to dssp204 3. chmod +x dssp204 4. sudo mv dssp204 /usr/local/bin/ 5. export DSSP=/usr/loca/bin/dssp204 6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2 What can be possibly wrong? Not sure, because what you're telling us isn't consistent: 1. You're not copying and pasting (or you are and you're setting variables wrong) because step 4 shows /usr/loca/bin as the location of the executable, which in step 3 you (presumably) put in /usr/local/bin (which actually makes sense). 2. That's not what you did because: dssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i /dev/null 2 /dev/null' says you have installed something called dssp20464 in /usr/bin. It's hard to troubleshoot something when you're not giving us consistent information. If the suffix 20464 indicates version 2.0.4 and 64-bit architecture, is that appropriate for your system? You have a 64-bit system, not 32-bit? -Justin The output is shown below: *Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single precision)Group 0 ( System) has 10901 elementsGroup 1 (Protein) has 121 elementsGroup 2 ( Protein-H) has 68 elementsGroup 3 (C-alpha) has16 elementsGroup 4 ( Backbone) has50 elementsGroup 5 ( MainChain) has 67 elementsGroup 6 ( MainChain+Cb) has67 elementsGroup 7 ( MainChain+H) has85 elementsGroup 8 ( SideChain) has36 elementsGroup 9 (SideChain-H) has 1 elementsGroup10 ( Prot-Masses) has 121 elementsGroup11 (non-Protein) has 10780 elementsGroup12 ( Other) has 2320 elementsGroup13 (RS1) has 2320 elementsGroup14 ( Water) has 8460 elementsGroup15 (SOL) has 8460 elementsGroup16 ( non-Water) has 2441 elementsSelect a group: 1Selected 1: 'Protein'There are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i /dev/null 2 /dev/null'Reading frame 0 time 0.000 Back Off! I just backed up ddUkWy9e to ./#ddUkWy9e.1#-- -Program gmx, VERSION 5.0.4Source code file: /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670Fatal error:Failed to execute command: Try specifying your dssp version with the -ver option.For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors- --* On Mon, Feb 16, 2015 at 6:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 6:20 PM, HANNIBAL LECTER wrote: Okay, so the same errors seem to be persisting. I am not sure what can possibly go wrong in this case. The dssp program seems to be working (just typing dssp in the shell gives information regarding the versions of dssp that has been used). The dsspold program doesn't seem to be doing much. No idea what that means, so I can't help with that. Does anyone know of a version of DSSP executable corresponding to a working Gromacs version? DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the other day), but in principle any 2.x version should work with GROMACS 4.6 or newer (the issue was closed 3 years ago, with minimal reported issues and no code modifications since). -Justin On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 4:07 PM, HANNIBAL LECTER wrote: Thanks for your reply. Couple of things. I don't really know where to get older dssp binaries. I couldn't find them available for download in the dssp website. http://swift.cmbi.ru.nl/gv/dssp/ Click on Distributions and at the bottom of that page, DSSPold is the old version. I renamed the mkdssp binary to dssp so I am sure nothing is wrong out there when I export the binaries for utilization in gromacs. Aside from the usual advice of making sure the binary is actually executable (and actually runs, check with ./dssp -V for instance), there's little to go
Re: [gmx-users] Regarding DSSP
Okay. what can be possibly wrong? I mean if someone CAN run Gromacs-5.0.4 + DSSP 2.0.4, it should be running in other systems as well unless I am messing something up. So I list my steps. 1. Download the executable from ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source code, but just the binaries). 2. rename the file to dssp204 3. chmod +x dssp204 4. sudo mv dssp204 /usr/local/bin/ 5. export DSSP=/usr/loca/bin/dssp204 6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2 What can be possibly wrong? The output is shown below: *Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single precision)Group 0 ( System) has 10901 elementsGroup 1 (Protein) has 121 elementsGroup 2 ( Protein-H) has 68 elementsGroup 3 (C-alpha) has16 elementsGroup 4 ( Backbone) has50 elementsGroup 5 ( MainChain) has67 elementsGroup 6 ( MainChain+Cb) has67 elementsGroup 7 ( MainChain+H) has85 elementsGroup 8 ( SideChain) has36 elementsGroup 9 (SideChain-H) has 1 elementsGroup10 ( Prot-Masses) has 121 elementsGroup11 (non-Protein) has 10780 elementsGroup12 ( Other) has 2320 elementsGroup13 (RS1) has 2320 elementsGroup14 ( Water) has 8460 elementsGroup15 (SOL) has 8460 elementsGroup16 ( non-Water) has 2441 elementsSelect a group: 1Selected 1: 'Protein'There are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i /dev/null 2 /dev/null'Reading frame 0 time 0.000 Back Off! I just backed up ddUkWy9e to ./#ddUkWy9e.1#---Program gmx, VERSION 5.0.4Source code file: /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670Fatal error:Failed to execute command: Try specifying your dssp version with the -ver option.For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors---* On Mon, Feb 16, 2015 at 6:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 6:20 PM, HANNIBAL LECTER wrote: Okay, so the same errors seem to be persisting. I am not sure what can possibly go wrong in this case. The dssp program seems to be working (just typing dssp in the shell gives information regarding the versions of dssp that has been used). The dsspold program doesn't seem to be doing much. No idea what that means, so I can't help with that. Does anyone know of a version of DSSP executable corresponding to a working Gromacs version? DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the other day), but in principle any 2.x version should work with GROMACS 4.6 or newer (the issue was closed 3 years ago, with minimal reported issues and no code modifications since). -Justin On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 4:07 PM, HANNIBAL LECTER wrote: Thanks for your reply. Couple of things. I don't really know where to get older dssp binaries. I couldn't find them available for download in the dssp website. http://swift.cmbi.ru.nl/gv/dssp/ Click on Distributions and at the bottom of that page, DSSPold is the old version. I renamed the mkdssp binary to dssp so I am sure nothing is wrong out there when I export the binaries for utilization in gromacs. Aside from the usual advice of making sure the binary is actually executable (and actually runs, check with ./dssp -V for instance), there's little to go on here. -Justin On Feb 16, 2015 3:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 3:15 PM, HANNIBAL LECTER wrote: Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is not a scope to specify using the -ver command in this particular version as opposed to the newer versions (5.0.4). By '' I meant do_dssp -f prot.xtc -s prot.tpr. How do I specify a dssp version in gromacs-4.5.6? I forget when the -ver flag was introduced. Safe bet is if you're using an ancient GROMACS version, you need a similarly ancient DSSP (version 1.0.x). Secondly, I did install Gromacs-5.0.4 for comparison, and I am using DSSP 2.0.4 again. This time I am using do_dssp -f prot.xtc -s prot.tpr -ver 2 The output I am getting is shown below. Not sure what is going on. *There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp -i ddJszHtZ -o ddRZ5pwg /dev/null 2 /dev/null'Reading frame 0 time My guess is that mkdssp is not actually the same thing as dssp - make sure you've installed a real, functional dssp binary. -Justin 0.000 Back Off
Re: [gmx-users] Regarding DSSP
Yes, the binary is working on a single pdb file. On Mon, Feb 16, 2015 at 7:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 6:55 PM, HANNIBAL LECTER wrote: Sorry, yes, I actually made a copy and pasted in the /usr/bin directory as well. So there IS actually a copy of the same program. Yes, my system is 64 bit. Just as a test case, I tried with the 32-bit version as well. Same error as above. Does the dssp binary work when you run it on a single .pdb file (as it's designed to do)? If not, then the binary is (somehow) incompatible with your machine. Compiling from source would fix that. -Justin On Mon, Feb 16, 2015 at 6:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 6:40 PM, HANNIBAL LECTER wrote: Okay. what can be possibly wrong? I mean if someone CAN run Gromacs-5.0.4 + DSSP 2.0.4, it should be running in other systems as well unless I am messing something up. So I list my steps. 1. Download the executable from ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source code, but just the binaries). 2. rename the file to dssp204 3. chmod +x dssp204 4. sudo mv dssp204 /usr/local/bin/ 5. export DSSP=/usr/loca/bin/dssp204 6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2 What can be possibly wrong? Not sure, because what you're telling us isn't consistent: 1. You're not copying and pasting (or you are and you're setting variables wrong) because step 4 shows /usr/loca/bin as the location of the executable, which in step 3 you (presumably) put in /usr/local/bin (which actually makes sense). 2. That's not what you did because: dssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i /dev/null 2 /dev/null' says you have installed something called dssp20464 in /usr/bin. It's hard to troubleshoot something when you're not giving us consistent information. If the suffix 20464 indicates version 2.0.4 and 64-bit architecture, is that appropriate for your system? You have a 64-bit system, not 32-bit? -Justin The output is shown below: *Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single precision)Group 0 ( System) has 10901 elementsGroup 1 (Protein) has 121 elementsGroup 2 ( Protein-H) has 68 elementsGroup 3 (C-alpha) has16 elementsGroup 4 ( Backbone) has50 elementsGroup 5 ( MainChain) has 67 elementsGroup 6 ( MainChain+Cb) has67 elementsGroup 7 ( MainChain+H) has85 elementsGroup 8 ( SideChain) has36 elementsGroup 9 (SideChain-H) has 1 elementsGroup10 ( Prot-Masses) has 121 elementsGroup11 (non-Protein) has 10780 elementsGroup12 ( Other) has 2320 elementsGroup13 (RS1) has 2320 elementsGroup14 ( Water) has 8460 elementsGroup15 (SOL) has 8460 elementsGroup16 ( non-Water) has 2441 elementsSelect a group: 1Selected 1: 'Protein'There are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i /dev/null 2 /dev/null'Reading frame 0 time 0.000 Back Off! I just backed up ddUkWy9e to ./#ddUkWy9e.1#-- -Program gmx, VERSION 5.0.4Source code file: /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670Fatal error:Failed to execute command: Try specifying your dssp version with the -ver option.For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors- --* On Mon, Feb 16, 2015 at 6:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 6:20 PM, HANNIBAL LECTER wrote: Okay, so the same errors seem to be persisting. I am not sure what can possibly go wrong in this case. The dssp program seems to be working (just typing dssp in the shell gives information regarding the versions of dssp that has been used). The dsspold program doesn't seem to be doing much. No idea what that means, so I can't help with that. Does anyone know of a version of DSSP executable corresponding to a working Gromacs version? DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the other day), but in principle any 2.x version should work with GROMACS 4.6 or newer (the issue was closed 3 years ago, with minimal reported issues and no code modifications since). -Justin On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 4:07 PM, HANNIBAL LECTER wrote: Thanks for your reply. Couple of things. I don't really know where to get older dssp binaries. I couldn't find them available for download in the dssp website. http
[gmx-users] Regarding DSSP
Hello all: I am not really sure, what are the various compatibility issues between the do_dssp program of different Gromacs versions and the versions of the DSSP program itself. I am trying to use dssp 2.0.4 and Gromacs 4.5.6. I have used export DSSP=/usr/bin/dssp and then do_dssp - I am getting Fatal error: Failed to execute command: /usr/bin/dssp -na ddMjYR8P ddfm1ecX /dev/null 2 /dev/null. Can someone please enlighten me about this? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with Lysozyme in Water Tutorial
It just means you either missed grompp -f ions.mdp ... OR the ions.mdp file is not there in the directory where you are performing your simulations. On Mon, Feb 2, 2015 at 12:10 PM, Stephen P. Molnar s.mol...@sbcglobal.net wrote: I have installed v-5.0.4 in Debian Wheezy without any warning or erroe messages. I have tried running the Lysozyme in Water Tutorial ( the one written for v-5) and have generated an error message in Step 4. The message is: File input/output error: ions.mdp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I checked the reference and did not find one [defaults] directive in the .itp file, let alone two Pleas advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and Multivariate www.FoundationForChemistry.com (614)312-7528(c) Skype: smolnar1 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] use of Walls in Martini simulations
What about electrostatics? Ewald summation is probably the culprit here. On Oct 24, 2014 12:05 PM, Ramon Reigada reig...@ub.edu wrote: Hi, I would like to post a question about simulating with Walls in gromacs and using the Martini force field. The question is very simple. I am trying to simulate a simple box of water molecules with pbc=xy and walls at z=0 and z=z_box. I use Berendsen T-coupling and no pressure bath. I am trying: pbc=xy nwall =2 wall_atomtype = C1 C1 (C1 are the alkane carbons defined in the martini force field file) wall_type = 9-3 wall_density = 110 110 wall_r_linpot = 1 and all what I have is that the initial box of water molecules breaks in two pieces that separate each other in the z-direction. The same result (or a segmentation fault) is obtained by using 10-4 o 12-6 LJ potentials, large wall_r_linpot values, other values of wall_densities, so I think that the problem is with the wall_atomtype. I tried the water bead (W) instead, and segmentation fault is obtained. thank you very much in advance, Ramon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Hamiltonian Replica Exchange
I would think of using Replica Exchange with Solute Tempering in this case. Look at the paper as to how one can implement this in Gromacs (doi: 10.1002/jcc.21703). Without having more details I would suggest to you to scale the Hamiltonian of each replica such that the Helix bundles are always correspond to the low temperature hamiltonian. The solute in your case would be the disordered ends that moves up the replica ladders during the exchange. The lambda dynamics module should be used and I would keep the topologies corresponding to the two ends such that at state B the hamiltonians of only the disordered ends are scaled (i.e. no scaling for the helical segments). On Tue, Jun 24, 2014 at 4:32 PM, Thomas Evangelidis teva...@gmail.com wrote: Greetings, I want to use the HREX implementation of GROMACS to study the dynamics of a heterodimeric protein. The structure is a two helix bundle (two helical monomers that are wrapped around each other) with disordered ends. I am mainly interested in the dynamics of the disordered ends because I know from NMR that the rest remains structured. My question is, can I scale selectively the Hamiltonian of the disordered ends whilst leaving the Hamiltonian of the rest of the protein untouched in order to preserve the dimeric structure? Otherwise I 'll have to impose distance and secondary structure restraints which will slow down the computations and render the dynamics of the structured part unphysical. Is it possible to increase the force constant of the harmonic restraints as lambda decreases to attenuate the stiffness of the helices? The other alternative will be to use much fewer replicas (up to lambda ~0.8 to be on the safe side) thus with slower sampling. thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] 答复: about exchange replica with replicas 140
Did you check the .err file as well? What does it say? How many cores do each node in the HPC have? There might be some issues with the supercomputer that you may be using? One of the nodes might have some issues which is probably causing the problem? I have used 300 cores for replica exchange simulations without any issues. On Thu, May 22, 2014 at 12:47 AM, #ZHANG HAIPING# hzhang...@e.ntu.edu.sgwrote: Dear Justin: The scripts I used is as follow: ## Set job parameters ## Job Name #BSUB -J OpenMPI ## Queue Name #BSUB -q medium_priority ## Output and Input Errors #BSUB -o job%J.out #BSUB -e job%J.err ## Specify walltime in HH:MM #BSUB -W 60:00 ## 16 Processors per Host #BSUB -R span[ptile=16] ## Requesting for 32 cores #BSUB -n 140 # Need to make our own machinefile MACHINEFILE=mymacs.$LSB_JOBID for i in `echo $LSB_HOSTS` do echo $i done $MACHINEFILE ## load module enviroement module load openmpi-1.6.5-intel-v12.1.5 module load intel-12.1.5 ## Run mpi program cd /gpfs/home/hzhang020/REMD/remdrun/scratch /usr/local/RH6_apps/openmpi-1.6.5-intel-v12.1.5/bin/mpirun --bind-to-core --report-bindings -np 140 -machinefile $MACHINEFILE /usr/local/RH6_apps/gromacs-4.6.2-double-intel/bin/mdrun_mpi_d -s prefix_.tpr -multi 140 -replex 3000 There was not obvious error information, just have the output file size is always 0. After long time, I kill it myself. NOTE: The load imbalance in PME FFT and solve is 384%. For optimal PME load balancing PME grid_x (1728) and grid_y (1728) should be divisible by #PME_nodes_x (2) and PME grid_y (1728) and grid_z (1728) should be divisible by #PME_nodes_y (1) NOTE: The load imbalance in PME FFT and solve is 384%. For optimal PME load balancing PME grid_x (1728) and grid_y (1728) should be divisible by #PME_nodes_x (2) and PME grid_y (1728) and grid_z (1728) should be divisible by #PME_nodes_y (1) -- WARNING: A process refused to die! Host: comp094 PID: 6751 This process may still be running and/or consuming resources. -- -- mpirun noticed that process rank 273 with PID 30914 on node comp122 exited on signal 9 (Killed). -- 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul jalem...@vt.edu 发送时间: 2014年5月22日 10:57 收件人: gmx-us...@gromacs.org 主题: Re: [gmx-users] about exchange replica with replicas 140 On 5/21/14, 10:53 PM, #ZHANG HAIPING# wrote: Dear gromacs user: I have encounter a problem when used HPC(high performance computer) to run replica exchange. I find that when I used replica over 128, it will not work, while under 128 , it is ok, even when I used cores much more than 128(several cores for one replica). The version I used is gromacs-4.6.2-double-intel. Hope for you help. You need to provide more information. Specifically, what commands are you issuing? What does will not work mean? Is there a specific error you are getting? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Nanoparticle topology
Parameters for metals are readily available in various forcefields in Gromacs. If your nanoparticles are gold spheres suspended freely in the system, then you can just get the parameters from from the forcefield files and specify the number of gold atoms in the topology file. On Wed, May 21, 2014 at 9:34 PM, guhansingh guhansi...@gmail.com wrote: Dear sir, I need to simulate gold nanoparticles (*NP*) interaction with some ligands (drugs). I can get ligand topology via ATB/ Prodrug server, but I can't get nanoparticle topology. Is there any external tools for *NP* modelling and topology generation.? Any other modifications to simulate metal atoms via GROMACS.? Thanks in advance -- Guhan.KA -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
You should provide with more information. The error message clearly states that there are multiple definitions for the moleculetype CU1. You should check carefully for redundancies in the top file On Wed, May 21, 2014 at 2:57 AM, Meenakshi Rajput ashi.rajpu...@gmail.comwrote: dear gromacs users I tried to add ions to my .gro file as it was showing the warning that:- System has non zero charge. But a new error occured when i run grompp command again:- Program grompp_d, VERSION 4.6.3 Source code file: /build/buildd/gromacs-4.6.3/src/kernel/toppush.c, line: 1412 Fatal error: moleculetype CU1 is redefined For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please help me... -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
