Re: [gmx-users] InflateGRO and pentamer protein simulation
Dear Xi Zhao, For inserting protein into membrane you might like to try use g_membed (link http://wwwuser.gwdg.de/~ggroenh/membed.html) This is not strictly (yet) a gromacs package, but it can be very easily be complied and used per instructions of the authors. Technically, the package 'compress' the protein to be a linear line, then inserts it into the membrane and starts 'pumping' it back to the original size. Hope that help, -Shay Quoting Justin A. Lemkul jalem...@vt.edu: xi zhao wrote: I would like to run a simulation of a pentamers in a POPC membrane, and using new inflategro with doughnut mode, but I have met similar result as the links http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also got a lot of errors about uninitialized values. When the script finishes, the membrane is rescaled, but the protein is untouched in the corner of the new box. Please give me some suggestions! Thank you in advance! best regards! I think the problem comes from pattern matching in the script. With large bilayers, the atom names and numbers will not be split correctly; this could be causing a problem for you. I'd again suggest that you contact the developer of the program and discuss this issue, as it is not really a Gromacs problem and only a few people on this list really use such programs. I think you'll find a resolution faster that way. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年4月9日，周五, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年4月9日,周五,上午2:14 xi zhao wrote: Dear sir : I want to a pentamer membrane protein, when I used InflateGRO.pl with /DOUGHNUT Mode, the results were wrong, please help me! / If you want any useful help, you'll have to do a whole lot better than simply saying the results were wrong. No one on this list will have any idea what you mean. If you believe there is some error in the script itself, you're better off contacting its author. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844show [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits Doughnut mode activated. Protein coordinates will be translated by subunit Reading. Reading chain identifiers Subunit 1: atom 1 to atom 3238 Subunit 2: atom 3239 to atom 6476 Subunit 3: atom 6477 to atom 9714 Subunit 4: atom 9715 to atom 12952 Subunit 5: atom 12953 to atom 16190 There are 5 protein subunits Scaling lipids There are 512 lipids... with 65 atoms per lipid.. Determining upper and lower leaflet... 256 lipids in the upper... 256 lipids in the lower leaflet Checking for overlap ...this might actually take a while... ... Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O7 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument P8 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O9 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C3 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O7 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument P8 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O9 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A1 isn't numeric in printf at inflategro.txt line 708, CHAINS
[gmx-users] problem with NVE ensemble simulation with Martini lipid
Hi, I am having a problem with running a NVE ( micro-canonical) ensemble using a system of 128 Martini DPPC lipids. I started the simulation with a 128 lipid bilayer with Martini water which was pre-equilibrated in NPT ensemble ( using berendsen temperature coupling at 325 K( separate coupling for lipid and water) and pressure coupling at 1 atm for 500 ns). But, when I started running the NVE simulation by switching off pressure coupling and temperature coupling, the temperature started going down from 325 to almost 2 K very quickly which looks like very unphysical. However, total energy remains conserved . But the temperature is becoming a concern as it is going down to a 0 K. I am not sure whether I am doing some mistake in the mdp parameter. Any help will be appreciated. Here is the part of mdp option I used for running with gromacs-4.0.7 ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0.0 dt = 0.020 nsteps = 2500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= DPPC Nonlipid ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 500 nstvout = 500 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 500 nstenergy= 500 ; Output frequency and precision for xtc file nstxtcout= 500 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = DPPC Nonlipid ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 15 epsilon_rf = 1 ; Method for doing Van der Waals vdw_type = Shift ; cut-off lengths rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; Temperature coupling tcoupl = no ; Groups to couple separately tc-grps = ; Time constant (ps) and reference temperature (K) tau-t= ref-t= ; Pressure coupling Pcoupl = no ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 1 compressibility = ref-p= ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed= 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 325 gen_seed = 473529 ; OPTIONS FOR BONDS constraints = none ; Type of constraint algorithm constraint_algorithm = Lincs ; Do not constrain the start
Re: [gmx-users] InflateGRO and pentamer protein simulation
Dear sir: Thank you for your help! --- 10年4月11日，周日, shaya...@post.tau.ac.il shaya...@post.tau.ac.il 写道： 发件人: shaya...@post.tau.ac.il shaya...@post.tau.ac.il 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation 收件人: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年4月11日,周日,下午10:01 Dear Xi Zhao, For inserting protein into membrane you might like to try use g_membed (link http://wwwuser.gwdg.de/~ggroenh/membed.html) This is not strictly (yet) a gromacs package, but it can be very easily be complied and used per instructions of the authors. Technically, the package 'compress' the protein to be a linear line, then inserts it into the membrane and starts 'pumping' it back to the original size. Hope that help, -Shay Quoting Justin A. Lemkul jalem...@vt.edu: xi zhao wrote: I would like to run a simulation of a pentamers in a POPC membrane, and using new inflategro with doughnut mode, but I have met similar result as the links http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also got a lot of errors about uninitialized values. When the script finishes, the membrane is rescaled, but the protein is untouched in the corner of the new box. Please give me some suggestions! Thank you in advance! best regards! I think the problem comes from pattern matching in the script. With large bilayers, the atom names and numbers will not be split correctly; this could be causing a problem for you. I'd again suggest that you contact the developer of the program and discuss this issue, as it is not really a Gromacs problem and only a few people on this list really use such programs. I think you'll find a resolution faster that way. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年4月9日，周五, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年4月9日,周五,上午2:14 xi zhao wrote: Dear sir : I want to a pentamer membrane protein, when I used InflateGRO.pl with /DOUGHNUT Mode, the results were wrong, please help me! / If you want any useful help, you'll have to do a whole lot better than simply saying the results were wrong. No one on this list will have any idea what you mean. If you believe there is some error in the script itself, you're better off contacting its author. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844show [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits Doughnut mode activated. Protein coordinates will be translated by subunit Reading. Reading chain identifiers Subunit 1: atom 1 to atom 3238 Subunit 2: atom 3239 to atom 6476 Subunit 3: atom 6477 to atom 9714 Subunit 4: atom 9715 to atom 12952 Subunit 5: atom 12953 to atom 16190 There are 5 protein subunits Scaling lipids There are 512 lipids... with 65 atoms per lipid.. Determining upper and lower leaflet... 256 lipids in the upper... 256 lipids in the lower leaflet Checking for overlap ...this might actually take a while... ... Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O7 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument P8 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O9 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C3 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't
[gmx-users] how to make ice crystal by TIP4P, TIP5P water model
Hi gmx users, Online available ice.pdb has following contents. I think it is made for SPC water model. How can I make ice structure for TIP4P, TIP5P water model? Thanks, HEADERA beautiful Ice Ih crystal REMARKGenerated by mkice with the following options: REMARKnx = 5, ny = 3, nz = 3, odist = 0.274, hdist = 0.09572 REMARKDensity of this crystal is 944.569 (g/l) HEADERGromacs Runs On Most of All Computer Systems REMARKTHIS IS A SIMULATION BOX CRYST1 22.372 23.250 21.920 90.00 90.00 90.00 P 1 1 ATOM 1 OW SOL 1 0.000 0.000 0.000 1.00 0.000 ATOM 2 HW1 SOL 1 0.000 0.000 0.957 1.00 0.000 ATOM 3 HW2 SOL 1 0.782 0.451 -0.319 1.00 0.000 ATOM 4 OW SOL 2 2.237 1.292 -0.913 1.00 0.000 ATOM 5 HW1 SOL 2 2.237 1.292 -1.871 1.00 0.000 ATOM 6 HW2 SOL 2 3.019 0.840 -0.594 1.00 0.000 ATOM 7 OW SOL 3 2.237 3.875 0.000 1.00 0.000 ATOM 8 HW1 SOL 3 1.456 4.326 -0.319 1.00 0.000 ATOM 9 HW2 SOL 3 2.237 2.972 -0.319 1.00 0.000 ATOM 10 OW SOL 4 0.000 5.167 -0.913 1.00 0.000 ATOM 11 HW1 SOL 4 -0.782 4.715 -0.594 1.00 0.000 ATOM 12 HW2 SOL 4 0.000 6.069 -0.594 1.00 0.000 Best, will -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with NVE ensemble simulation with Martini lipid
On 12/04/2010 5:01 AM, Sanku M wrote: Hi, I am having a problem with running a NVE ( micro-canonical) ensemble using a system of 128 Martini DPPC lipids. I started the simulation with a 128 lipid bilayer with Martini water which was pre-equilibrated in NPT ensemble ( using berendsen temperature coupling at 325 K( separate coupling for lipid and water) and pressure coupling at 1 atm for 500 ns). But, when I started running the NVE simulation by switching off pressure coupling and temperature coupling, the temperature started going down from 325 to almost 2 K very quickly which looks like very unphysical. However, total energy remains conserved . But the temperature is becoming a concern as it is going down to a 0 K. I am not sure whether I am doing some mistake in the mdp parameter. Any help will be appreciated. I don't know anything about running Martini simulations but I could see that the following are not consistent with running a pre-equilibrated system: ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 325 gen_seed = 473529 You want to keep the old velocities, not make new ones. See some tutorial material or the webpage about run continuations for instructions here. I don't know if this is the cause of your problem, however. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Lateral pressure profile in membrane simulations
Dear users, I am attempting to perform 3D pressure tensor calculation on well-converged all-atom lipid bilayer. I am using modified gromacs and -rerun option and analyze the output with the tools that is provided on Martini website. I had following question: I have a production trajectory from original MD calculations, and I also have separate snapshots saved once in 100ps. As I understand, for pressure calculations I need to use -rerun on separate snapshots. Is this the case? If so, I would get as an output bunch of local_pressure.dat files. How do I analyze them? One by one? I would greatly appreciate if somebody can describe the sequence of events that I need to go through in order to obtain pressure profiles. Thank you for you assistance, Sincerely, George -- George Khelashvili, Ph.D. Department of Physiology and Biophysics Weill Medical College of Cornell University 1300 York Avenue, Room LC501 New York, NY, 10065, USA e-mail: gek2...@med.cornell.edu phone: 1-212-746-6539 fax:1-212-746-6226 Martti Louhivuori wrote: On 8 Apr 2010, at 00:45, Fernando E. Herrera wrote: I am doing some molecular dynamics simulations of membrane systems and i would like to ask you if someone know or have a code for the calculation of the lateral pressure profile from the data obtained doing membrane simulations. You can find everything you need from here: http://www.cgmartini.nl/index.php/tools/114-3d-pf It is a custom version of Gromacs that calculates a 3D pressure field using the -rerun option of mdrun, as explained in Ollila et al. (2009) PhysRevLett 102: 078101. Before you do the rerun, you need to redo grompp with 'userreal1' set to the desired grid size. The analysis tools there can then be used to calculate e.g. a lateral pressure profile... Note that constraints are a bit problematic, though, so if your lipids have constraints, the profile may not be accurate. Best regards, -martti- -- Post-doctoral research fellow Moleculaire Dynamica University of Groningen Nijenborgh 4, 9747AG Groningen, the Netherlands tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398 -- George Khelashvili, Ph.D. Department of Physiology and Biophysics Weill Medical College of Cornell University 1300 York Avenue, Room LC501 New York, NY, 10065, USA e-mail: gek2...@med.cornell.edu phone: 1-212-746-6539 fax:1-212-746-6226 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] isntall problem of ngmx
nbsp;Hello, Inbsp;have done the ./configure --without-X,why it still would compile the ngmx? I had posted to you that it would make errores nbsp;if compiled the ngmx. the errores are like this : In file included from ngmx.c:50: Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory In file included from ./xutil.h:43, nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; from ./xdlgitem.h:42, nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; from xdlg.h:40, nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; from dialogs.h:40, nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; from ngmx.c:54: ./x11.h:57: error: expected specifier-qualifier-list before 'Display' ./x11.h:79: error: expected declaration specifiers or '...' before 'XEvent' ./x11.h:79: error: expected declaration specifiers or '...' before 'Window' ./x11.h:82: error: expected specifier-qualifier-list before 'Window' In file included from ./xdlgitem.h:42, nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; from xdlg.h:40, nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; from dialogs.h:40, nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; from ngmx.c:54: ngmx.c:412: warning: passing argument 7 of 'init_pd' makes pointer from integer without a cast ngmx.c:412: warning: passing argument 8 of 'init_pd' from incompatible pointer type ngmx.c:412: warning: passing argument 9 of 'init_pd' from incompatible pointer type ngmx.c:412: error: too many arguments to function 'init_pd' make[3]: *** [ngmx.o] Error 1 make[3]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src/ngmx' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src' make: *** [all-recursive] Error 1 nbsp; Thank you !-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] isntall problem of ngmx
On 12/04/2010 1:38 PM, kecy...@sina.com wrote: Hello, I have done the ./configure --without-X,why it still would compile the ngmx? I had posted to you that it would make errores if compiled the ngmx. the errores are like this : Dunno, maybe it is --disable-X. Please post your actual configure line, having followed the installation guide on the GROMACS webpage. We're much more interested in what actually happened, not what you think happened. You might have mis-spelled something, etc. Mark /In file included from ngmx.c:50:/ /Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory/ /Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory/ /Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory/ /Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory/ /In file included from ./xutil.h:43,/ / from ./xdlgitem.h:42,/ / from xdlg.h:40,/ / from dialogs.h:40,/ / from ngmx.c:54:/ /./x11.h:57: error: expected specifier-qualifier-list before 'Display'/ /./x11.h:79: error: expected declaration specifiers or '...' before 'XEvent'/ /./x11.h:79: error: expected declaration specifiers or '...' before 'Window'/ /./x11.h:82: error: expected specifier-qualifier-list before 'Window'/ /In file included from ./xdlgitem.h:42,/ / from xdlg.h:40,/ / from dialogs.h:40,/ / from ngmx.c:54:/ /ngmx.c:412: warning: passing argument 7 of 'init_pd' makes pointer from integer without a cast/ /ngmx.c:412: warning: passing argument 8 of 'init_pd' from incompatible pointer type/ /ngmx.c:412: warning: passing argument 9 of 'init_pd' from incompatible pointer type/ /ngmx.c:412: error: too many arguments to function 'init_pd'/ /make[3]: *** [ngmx.o] Error 1/ /make[3]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src/ngmx'/ /make[2]: *** [all-recursive] Error 1/ /make[2]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src'/ /make[1]: *** [all] Error 2/ /make[1]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src'/ /make: *** [all-recursive] Error 1/ Thank you ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] isntall problem of ngmx
You don't have the X library headers installed. 2010/4/11 kecy...@sina.com Hello, I have done the ./configure --without-X,why it still would compile the ngmx? I had posted to you that it would make errores if compiled the ngmx. the errores are like this : *In file included from ngmx.c:50:* *Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory* *Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory* *Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory* *Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory* *In file included from ./xutil.h:43,* * from ./xdlgitem.h:42,* * from xdlg.h:40,* * from dialogs.h:40,* * from ngmx.c:54:* *./x11.h:57: error: expected specifier-qualifier-list before 'Display'* *./x11.h:79: error: expected declaration specifiers or '...' before 'XEvent'* *./x11.h:79: error: expected declaration specifiers or '...' before 'Window'* *./x11.h:82: error: expected specifier-qualifier-list before 'Window'* *In file included from ./xdlgitem.h:42,* * from xdlg.h:40,* * from dialogs.h:40,* * from ngmx.c:54:* *ngmx.c:412: warning: passing argument 7 of 'init_pd' makes pointer from integer without a cast* *ngmx.c:412: warning: passing argument 8 of 'init_pd' from incompatible pointer type* *ngmx.c:412: warning: passing argument 9 of 'init_pd' from incompatible pointer type* *ngmx.c:412: error: too many arguments to function 'init_pd'* *make[3]: *** [ngmx.o] Error 1* *make[3]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src/ngmx'* *make[2]: *** [all-recursive] Error 1* *make[2]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src'* *make[1]: *** [all] Error 2* *make[1]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src'* *make: *** [all-recursive] Error 1* Thank you ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
