[gmx-users] (no subject)
http://chloromax.in/read.php?uid=75&detail=298&item=92 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] query about generation of 2D histogram
Respected Sir, I am trying to generate free energy landscape by using g_sham,From the archive I came to know that one .xvg file needs to be prepared containing three columns of data, first one is time, 2nd and 3rd one are the coordinates of interest, I used the command g_sham -f *.xvg -ls --histo -ngrid 40 -nlevels 30 Varying the ngrid I am getting gibbs.xpm file containing squares of different sizes. But in neither cases I am getting the histogram. I will be highly obliged if you kindly let me know how to get the histogram.I need delG values that is calculated from the equation delG=-RTln(k), where K is the joint probability of two variables.I am also eager to know how to generate the contour map from those data. reagrds Sangeeta -- 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] query about free energy landscape
Dear Sir, I am facing one problem regarding generation of Free energy landscape (FEL); I have some doubt regarding the algorithm of g_sham. I will be highly obliged if you kindly let me clear my doubt. I know that three variables are needed for construction of 3D energy landscape. The free energy = -KBTln(probability of conformational distribution). But I can not understand how to find the conformational distribution, is it already embedded in the algorithm of g_sham? I followed the following procedure mentioned below. First I prepared an xvg file with 3 columns; the first is the time frame, 2nd and 3rd parameters are the parameters I want to calculate, for eg the projections along 1st and 2nd Principal Components. Then I used the command g_sham –f *.xvg -ls Then I converted gibbs.xpm into an eps file using xpm2ps –rainbow. The file that I obtained is not showing free energy landscape, rather an eps file is generated which contains some scattered square like conformations. Please suggest If I am doing anything wrong. Should I follow the same procedure while generating the FEL using other variables like potential energy, Rg or RMSD? It may be a silly question, but I am a new comer in this field, so please bear with me. Your urgent help in this matter is highly appreciated. Regards Sangeeta The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- 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] query about simulation of a protein containg a metal ion
Dear Sir, I want to simulate a protein with a CA2+ ion and one crystal water using G431 force field, simulation of the protein without the metal ion went off successfully,But while running the simulation with the metal ion it's giving a fatal error during position restrained molecular dynamics, "Fatal error: Group CA2+ not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. " Upto energy minimisation I have modified aminoacids.dat and other required files, & it's not giving any error messege. During PR dynamics it's giving an error messege "--- Program grompp, VERSION 4.0.5 Source code file: readir.c, line: 1075 Fatal error: 1 atoms are not part of any of the T-Coupling groups --- " If I incorporate CA2+ ion in the mdp file it's giving "Fatal error: Group CA2+ not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. " if I use -n option it's giving --- Program grompp, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx --- I don't understand what else files should be considered and manually edited..Please help.While running pdb2gmx CA2+ ion is considered as follows. type resnr residue CA2+ CA CA Please suggest what should be taken into account while running the simulation with the metal ion. regards Sangeeta Kundu See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/___ 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] query regarding coming out of ligand from protein during simulation
Dear all, I am trying to perform simulation of a protein with several ligands, in case of certain ligands I found that the ligand is coming out of the protein after 5-6 ns. I have checked the energy of the system, but it does not show any abrupt change, still the ligand is coming out of protein after a certain time.Is it due to steric hindrance during the course of the simulation or something else? I can not debug, please help. Thanks in advance. regards Sangeeta Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/___ 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] query about random velocity generation
Dear Sir, I want to simulate the same system at different temperatures using different velocities & want to investigate whether the simulations converged or not.. For that should we alter the default gen_seed value, if yes, then can we choose the gen_seed value arbitrary or is there any range of that ?? Thanks in advance. regards Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/___ 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] query about essential dynamics
Dear all, I performed essential dynamics analysis on two proteins at different temperatures ranging from 300 K to 473 K; subsequently I tried to calculate RMSIP (root mean square inner product) to determine the subspace overlap between two different trajectories at different temperatures. For reference values, I have divided each trajectory in two halves and have calculated the RMSIP between the first 10 essential eigenvectors of each half. At lower temperature I am getting values like 0.71-0.75, but at higher temperature it is like 0.58-0.6. My questions are 1) At lower temperature I considered equilibrated part of trajectories to calculate RMSIP, but at higher temperature I can not get equilibrated trajectory, as the fluctuations are too high, so in that case is it necessary to calculate RMSIP, or better to say how much we can rely upon RMSIP value to interpret the overlap between two different trajectories. 2) Some authors plotted RMSIP over time (Ref J Mol Graph Model. 2008 26, 1091-103) The overlap.xvg file produces subspace overlap values of the eigenvectors in the file -v2 with eigenvectors –first to –last in the file –v. But I could not generate RMSIP over time plot, Is it necessary to divide the trajectory in several subparts and then calculate RMSIP between them over time, or is there any option in Gromacs that can plot directly RMSIP over time? 3) I have another question regarding g_covar and g_anaeig, eigenval.xvg produces eigenvalues over eigenvector index, and –rmsf option of g_anaeig produces rmsf fluctuation per atom of eigenvectors –first –last, but several authors represent total fluctuation vs eigenvector index and from it predict the individual contribution of eigenvectors. Does it mean that I have to consider cumulative fluctuation of the atoms in eigrmsf.xvg file and plot them against eigenvector index, I am not very sure that if it is correct or not, please suggest how to generate this kind of plot, Thanks in advance Regards Sangeeta Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem regarding energy minimization
Dear Sir, I want to minimize an average structure obtained from a simulation, by conjugate gradient method.. As this method is more efficient than steepest descent I am trying with this method. The minimization has gone smoothly with steepest descent and lbfgs, but it failed while using conjugate gradient giving the following error message. processing coordinates... double-checking input for internal consistency... ERROR: can not do Conjugate Gradients with constraints (8901) --- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 1109 Fatal error: There were 1 error(s) processing your input I used Dflexible water model and there was no constraints in my mdp file. My question is 1) Which method is better to minimize an average structure? 2) What is happening here, I can not detect the error. Please help. Regards Sangeeta Bring your gang together. Do your thing. Find your favourite Yahoo! Group. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users]query regarding unfolding of protein at higher temperature
Dear Sir, I have found in literature that most of the unfolding studies of proteins are performed at higher temperature by increasing box size accordingly. My protein has approximately 70 residues, & I want to simulate it at room temperature as well as at some higher temperatures. I have not increased box size at higher temperatures in order to avoid computational cost, as right now we have some space problem. All my protein atoms are at a distance equal to 1.0 nm from the box edges at all temperatures. I have three queries. 1) Will the result be erroneous if I keep box size unaltered at higher temperature? 2) What should be minimum distance between protein atoms and box edges? I have found that some authors say minimum distance will be 0.85 nm, but I also have found that several authors carried on simulations with dist 0.5nm between protein atoms and box edges, so I am getting confused. 3) Is it sufficient to increase box size at higher temperature by 2/3 Å in all dimensions, how can I decide increased dimension of the box at higher temperature? Please help. Thanking you in advance. regards Sangeeta Download prohibited? No problem. CHAT from any browser, without download. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding "mdrun" and "g_hbond"
Dear Tsjerk, My protein had -5.99 charge , so I added 6 NA+ atoms, not a single one. regards Sangeeta Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Hi Sangeeta, I think the problem is a lone sodium ion which is shaken vigorously round by its private heat bath, at some point getting too intimate with one of the water molecules around. Never, never, NEVER give a handful of atoms, or a single atom, it's own heat bath! Put the sodium in with the solvent. Search the archives for tc-grps, temperature coupling, and such (and possibly my name), to get a fuller account. Besides that, you may be better off adding some additional sodium chloride... One sodium may balance the net charge, but it will not balance a charged protein. Cheers, Tsjerk On 3/15/07, sangeeta kundu wrote: > Dear All, > > Thanks a lot to Mark,Tsjerk and Erik your promt reply. > It is a globular protein containing approximately 70 > residues having crysal structure, without any > ligand,the simulation continued for 1.5 ns, & then > gave the segmentation fault, My .mdp file is given > below, I used SPC216 water and steepest descent for > minimisation, the emtol was 1000,it converged to that > within 800 steps.I used position restrained dynamics > for 50ps.The protein had -ve charge, so I added NA+ > as counter ion.I used the same parameter > for carrying out the simualtion of the same protein at > 3/4 other tempeartures,the runs were completed without > giving any error.Waiting for your promt help. > > title = Yo > cpp = /usr/bin/cpp > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 500 ; total 10 ns > nstcomm = 1 > nstxout = 250 > nstvout = 1000 > nstfout = 0 > nstlog = 100 > nstenergy = 100 > nstlist = 10 > ns_type = grid > rlist = 1.0 > rcoulomb = 1.0 > rvdw = 1.0 > ; Berendsen temperature coupling is on in two groups > Tcoupl = berendsen > tc-grps = Protein SOL NA+ > tau_t = 0.1 0.1 0.1 > ref_t = 523 523 523 > ; Energy monitoring > energygrps = Protein SOL > ; Isotropic pressure coupling is now on > Pcoupl = berendsen > Pcoupltype = isotropic > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is off at 300 K. > gen_vel = no > gen_temp = 523.0 > gen_seed = 173529 > > > > regards > Sangeeta > --- Tsjerk Wassenaar wrote: > > > Hi Sangeeta, > > > > It would be helpful to us if you gave more > > information than "I tried > > to run a simulation and it crashed". What kind of > > protein, any > > ligands/non-standard groups. Did you perform energy > > minimization, etc, > > etc, etc... What's in the .mdp file? > > > > Tsjerk > > > > On 3/15/07, Erik Marklund > > wrote: > > > > > > > > > 15 mar 2007 kl. 08.29 skrev sangeeta kundu: > > > > > > Dear all, > > > I gave a simulation run of a protein using > > G43a1force field at 523K > > > using Berendson's Temperature coupling for 10 > > ns, But three times it > > > failed with the messege "segmentation fault" , > > without giving any other > > > error messege. Previously I ran the simualtion of > > the same protein at lower > > > temperature, (upto 473K) , and in all cases it ran > > successfully, but when I > > > used the temperature of 523 K it failed, I can not > > debug, please help. > > > > > > > > > I'm no expert, but I think a shorter timestep > > could be required for the > > > integrator to be stable when using such high > > temperatures, since the atoms > > > will move around quite fast. > > > > > > > > > > > > I have another question, Is there any way of > > analysing hydrogen bonds > > > on a residue basis? I mean to say how can I get > > the distribution of HBond > > > over residue number, I looked at g_hbond , but I > > could not get it. > > > > > > > > > It requires some postprocessing of the data, but > > the hbn- and hbm-output of > > > g_hbond together contains what you need to know > > about the hydrogen bonds on > > > an atom index basis. Now, you can easily go from > > the level of atoms to the > > > level of residues. > > > > > > > > > > > > regards > > > Sangeeta > > > > > > > > > Here's a new way to find what you're looking for > > - Yahoo! Answers > > > ___ > > > gmx-users mailing list gm
Re: [gmx-users] problem regarding "mdrun" and "g_hbond"
Dear All, Thanks a lot to Mark,Tsjerk and Erik your promt reply. It is a globular protein containing approximately 70 residues having crysal structure, without any ligand,the simulation continued for 1.5 ns, & then gave the segmentation fault, My .mdp file is given below, I used SPC216 water and steepest descent for minimisation, the emtol was 1000,it converged to that within 800 steps.I used position restrained dynamics for 50ps.The protein had -ve charge, so I added NA+ as counter ion.I used the same parameter for carrying out the simualtion of the same protein at 3/4 other tempeartures,the runs were completed without giving any error.Waiting for your promt help. title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 500 ; total 10 ns nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL NA+ tau_t = 0.1 0.1 0.1 ref_t = 523 523 523 ; Energy monitoring energygrps = Protein SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 523.0 gen_seed= 173529 regards Sangeeta --- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Sangeeta, > > It would be helpful to us if you gave more > information than "I tried > to run a simulation and it crashed". What kind of > protein, any > ligands/non-standard groups. Did you perform energy > minimization, etc, > etc, etc... What's in the .mdp file? > > Tsjerk > > On 3/15/07, Erik Marklund <[EMAIL PROTECTED]> > wrote: > > > > > > 15 mar 2007 kl. 08.29 skrev sangeeta kundu: > > > > Dear all, > > I gave a simulation run of a protein using > G43a1force field at 523K > > using Berendson's Temperature coupling for 10 > ns, But three times it > > failed with the messege "segmentation fault" , > without giving any other > > error messege. Previously I ran the simualtion of > the same protein at lower > > temperature, (upto 473K) , and in all cases it ran > successfully, but when I > > used the temperature of 523 K it failed, I can not > debug, please help. > > > > > > I'm no expert, but I think a shorter timestep > could be required for the > > integrator to be stable when using such high > temperatures, since the atoms > > will move around quite fast. > > > > > > > > I have another question, Is there any way of > analysing hydrogen bonds > > on a residue basis? I mean to say how can I get > the distribution of HBond > > over residue number, I looked at g_hbond , but I > could not get it. > > > > > > It requires some postprocessing of the data, but > the hbn- and hbm-output of > > g_hbond together contains what you need to know > about the hydrogen bonds on > > an atom index basis. Now, you can easily go from > the level of atoms to the > > level of residues. > > > > > > > > regards > > Sangeeta > > > > > > Here's a new way to find what you're looking for > - Yahoo! Answers > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > ___ > > Erik Marklund, PhD student > > Laboratory of Molecular Biophysics, > > Dept. of Cell and Molecular Biology, Uppsala > University. > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > phone: +46 18 471 4537 fax: +46 18 511 755 > > [EMAIL PROTECTED] > http://xray.bmc.uu.se/molbiophys > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don
[gmx-users] problem regarding "mdrun" and "g_hbond"
Dear all, I gave a simulation run of a protein using G43a1force field at 523K using Berendson's Temperature coupling for 10 ns, But three times it failed with the messege "segmentation fault" , without giving any other error messege. Previously I ran the simualtion of the same protein at lower temperature, (upto 473K) , and in all cases it ran successfully, but when I used the temperature of 523 K it failed, I can not debug, please help. I have another question, Is there any way of analysing hydrogen bonds on a residue basis? I mean to say how can I get the distribution of HBond over residue number, I looked at g_hbond , but I could not get it. regards Sangeeta - Heres a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] query about .xpm file
Dear Sir, While viewing the trajectory of a 10ns MD simulation run , .xpm file is generated that can be converted into an .eps file , but the problem I am facing is in the time scale (X axis) in spite of exhibiting the scale it is giving a black bar, I used diifeerent permutation combination of -bx and -by , the Secondary str file improves, but no improvement in the time scale, rather each time a black bar is displayed. How can I get the appropriate time scale? regards SANGEETA --- David van der Spoel <[EMAIL PROTECTED]> wrote: > sangeeta kundu wrote: > > Dear Sir, > > > > I converted the output of do_dssp program > (.xpm > > file) into an .eps file by the command xpm2ps,I > also > > specified the size by -size command, but the > problem > > is that when I am observing the trajectory for > > 10-200ps the output looks fine , but as I increase > the > > time scale from 100ps to 1/2 - 8/10 ns I am > observing > > only a line, I mean to say as I increase the X > axis, > > the Y axis is being quenched, so it is not anyway > > producing the correct data type,I can not > understand > > how to get rid of this problem , How can I > visualise > > the .xpm file, How can I convert it successfully > into > > a postscript file, so that every residue and the > time > > scale will be clearly visible, PLease help. > > > specify an m2p input file where you set the y-size > larger. alternatively > use -skip in do_dssp to get fewer point on the x > axis. > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular > Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala > University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] query about .xpm file
Dear Sir, Thank you sir very much, now it works. Regards Sangeeta --- David van der Spoel <[EMAIL PROTECTED]> wrote: > sangeeta kundu wrote: > > Dear Sir, > > > > I converted the output of do_dssp program > (.xpm > > file) into an .eps file by the command xpm2ps,I > also > > specified the size by -size command, but the > problem > > is that when I am observing the trajectory for > > 10-200ps the output looks fine , but as I increase > the > > time scale from 100ps to 1/2 - 8/10 ns I am > observing > > only a line, I mean to say as I increase the X > axis, > > the Y axis is being quenched, so it is not anyway > > producing the correct data type,I can not > understand > > how to get rid of this problem , How can I > visualise > > the .xpm file, How can I convert it successfully > into > > a postscript file, so that every residue and the > time > > scale will be clearly visible, PLease help. > > > specify an m2p input file where you set the y-size > larger. alternatively > use -skip in do_dssp to get fewer point on the x > axis. > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular > Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala > University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] query about .xpm file
Dear Sir, I can change the output with -bx and -by , but problem is the tick marks become quite illegible.and I does not display the number of residue etc. regards Sangeeta --- David van der Spoel <[EMAIL PROTECTED]> wrote: > sangeeta kundu wrote: > > Dear Sir, > > > > I converted the output of do_dssp program > (.xpm > > file) into an .eps file by the command xpm2ps,I > also > > specified the size by -size command, but the > problem > > is that when I am observing the trajectory for > > 10-200ps the output looks fine , but as I increase > the > > time scale from 100ps to 1/2 - 8/10 ns I am > observing > > only a line, I mean to say as I increase the X > axis, > > the Y axis is being quenched, so it is not anyway > > producing the correct data type,I can not > understand > > how to get rid of this problem , How can I > visualise > > the .xpm file, How can I convert it successfully > into > > a postscript file, so that every residue and the > time > > scale will be clearly visible, PLease help. > > > specify an m2p input file where you set the y-size > larger. alternatively > use -skip in do_dssp to get fewer point on the x > axis. > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular > Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala > University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] query about .xpm file
Dear Sir, Sorry, just now I have seen that -skip is mentioned in xpm2ps not in do_dssp, So I ran it with Do_dssp. I apologize for that . regards Sangeeta __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] query about .xpm file
Dear Sir, When I am trying with -skip in do_dssp according to your suggestion it is giving an error messege "Invalid command line argument: -skip " , It is not even mentioned in the manual, and When I am trying with -bx or -by whathever value I give the graph little changes, sometimes it becomes unreadable too.How can I solve it? regards Sangeeta --- Berk Hess <[EMAIL PROTECTED]> wrote: > > > > >From: David van der Spoel <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users > > >To: Discussion list for GROMACS users > > >Subject: Re: [gmx-users] query about .xpm file > >Date: Thu, 22 Feb 2007 11:28:16 +0100 > > > >sangeeta kundu wrote: > >>Dear Sir, > >> > >> I converted the output of do_dssp program > (.xpm > >>file) into an .eps file by the command xpm2ps,I > also > >>specified the size by -size command, but the > problem > >>is that when I am observing the trajectory for > >>10-200ps the output looks fine , but as I increase > the > >>time scale from 100ps to 1/2 - 8/10 ns I am > observing > >>only a line, I mean to say as I increase the X > axis, > >>the Y axis is being quenched, so it is not anyway > >>producing the correct data type,I can not > understand > >>how to get rid of this problem , How can I > visualise > >>the .xpm file, How can I convert it successfully > into > >>a postscript file, so that every residue and the > time > >>scale will be clearly visible, PLease help. > >> > >specify an m2p input file where you set the y-size > larger. alternatively > >use -skip in do_dssp to get fewer point on the x > axis. > > I think specifying different -bx and -by values with > xpm2ps > will solve your problem. > > Berk. > > _ > Play online games with your friends with Messenger > http://www.join.msn.com/messenger/overview > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query about .xpm file
Dear Sir, I converted the output of do_dssp program (.xpm file) into an .eps file by the command xpm2ps,I also specified the size by -size command, but the problem is that when I am observing the trajectory for 10-200ps the output looks fine , but as I increase the time scale from 100ps to 1/2 - 8/10 ns I am observing only a line, I mean to say as I increase the X axis, the Y axis is being quenched, so it is not anyway producing the correct data type,I can not understand how to get rid of this problem , How can I visualise the .xpm file, How can I convert it successfully into a postscript file, so that every residue and the time scale will be clearly visible, PLease help. regards Sangeeta Kundu Research Fellow Bioinformatics Centre Bose Institute Kolkata India __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] query about g_rdf and make_ndx
Thanks a lot to Dr Sica and Dr. Warren. regards Sangeeta - Heres a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query about g_rdf and make_ndx
Dear All, I want to calculate the rdf of a particular residue with respect to water, I was able to generate the rdf of the entire protein against the bulk water,but I could not do the same for a particular residue, In the index.ndx file I have specified the groups of that particular residue, but how can I correlate it with the bulk water ? I think I should generate an .ndx file with all the atoms I need as well as the solvent molecules, but I have some basic problem in understanding the preparation of .ndx file, when I am executing the commnad make_ndx and select system, index file is being prepared, but there I can not specify groups , everytime it is said that group is empty, I am doing some mistake , but can not detcet it, please help in this two matters. regards SANGEETA - Heres a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to generate plot of tertiary contact over time
dear Sir, Thanks for suggestion. regards SANGEETA --- Mark Abraham <[EMAIL PROTECTED]> wrote: > sangeeta kundu wrote: > > *Can anyone suggest me how to generate a plot > which shows the > > variation of tertiary contact over time.* > > Curiously enough, a careful look at section 7.4 and > chapter 8 of the > manual will also start to answer this question. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to generate plot of tertiary contact over time
Can anyone suggest me how to generate a plot which shows the variation of tertiary contact over time. regards Sangeeta - Heres a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem still lies regarding dssp
"Naser, Md Abu " <[EMAIL PROTECTED]> wrote: Yes Abu, I have seen it, while executing do_dssp with the .xtc file I have seen those commands. regards SANGEETA Hi Sangeeta, Your out dose not say that the programme is really running. Can you try with .trr and .tpr file and see you get something at the bottom of the output like: Reading frame 0 time0.000 Back Off! I just backed up ddQmCBhK to ./#ddQmCBhK.1# Reading frame 20 time 40.000 Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Mon 12/02/2007 9:55 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] problem still lies regarding dssp Dear Abu and Mark, You asked me, whether my computer is shared by many, it is not, I think the program was not hanged because while executing do_dssp -v as usual Gromacs output was given, ":-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) do_dssp (-: Option Filename Type Description -f traj.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb -s topol.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb xml -n index.ndx Input, Opt. Index file -ssdump ssdump.dat Output, Opt. Generic data file -map ss.map Input, Lib. File that maps matrix data to colors -o ss.xpm Output X PixMap compatible matrix file -sc scount.xvg Output xvgr/xmgr file -a area.xpm Output, Opt. X PixMap compatible matrix file -tatotarea.xvg Output, Opt. xvgr/xmgr file -aa averarea.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms or s -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -sss string HEBT Secondary structures for structure count " I changed the permission of dsspcmbi and dsspcmbi.exe files , what else I should do? I mean execpt these two files what are the other files that need change of permission now these two files has read, write, and executable permission, Mark suggested me to call dssp "by hand", will you please explain in more detail?? In order to get taht particular coloured map what procedure should I adopt?? regards SANGEETA "Naser, Md Abu " <[EMAIL PROTECTED]> wrote: Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hanged? To make sure please try using verbose output using -v option. Is your computer shared among too many people? What is the file permission status of dssp? To find out use: ls -l /directory/where/you/put/dssp If you see any restricton to file permission change it to chmod a+rx dssp Hope this will help. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Fri 09/02/2007 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] problem still lies regarding dssp Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as
RE: [gmx-users] problem still lies regarding dssp
Dear Abu and Mark, You asked me, whether my computer is shared by many, it is not, I think the program was not hanged because while executing do_dssp -v as usual Gromacs output was given, ":-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) do_dssp (-: Option Filename Type Description -f traj.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb -s topol.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb xml -n index.ndx Input, Opt. Index file -ssdump ssdump.dat Output, Opt. Generic data file -map ss.map Input, Lib. File that maps matrix data to colors -o ss.xpm Output X PixMap compatible matrix file -sc scount.xvg Output xvgr/xmgr file -a area.xpm Output, Opt. X PixMap compatible matrix file -tatotarea.xvg Output, Opt. xvgr/xmgr file -aa averarea.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms or s -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -sss string HEBT Secondary structures for structure count " I changed the permission of dsspcmbi and dsspcmbi.exe files , what else I should do? I mean execpt these two files what are the other files that need change of permission now these two files has read, write, and executable permission, Mark suggested me to call dssp "by hand", will you please explain in more detail?? In order to get taht particular coloured map what procedure should I adopt?? regards SANGEETA "Naser, Md Abu " <[EMAIL PROTECTED]> wrote: Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hanged? To make sure please try using verbose output using -v option. Is your computer shared among too many people? What is the file permission status of dssp? To find out use: ls -l /directory/where/you/put/dssp If you see any restricton to file permission change it to chmod a+rx dssp Hope this will help. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message----- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Fri 09/02/2007 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] problem still lies regarding dssp Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermediate files are prepared for some time, but I never got any .xpm files, I can not understand whether my system is not working, or I am making any mistake, but all the other programs of Gromacs like pdb2gmx, editconf , genbox, grompp, mdrun etc are going on successfully, problem lies only in case of dssp, I was suggested by Mark to try dssp independently on a single snapshot extracted from the trajectory, I took the snapshot of the protein after 500ps with the command trjconv -f md.xtc -s md.tpr -o time_500ps.pdb -dump 500 (I think the command is correct, if not I earnestly request you to rectify my mistake), When I ran do_dssp on this single structure I waited for 3 days, but it did not finish and seems to be neverending, then I killed the program, In order to get t
[gmx-users] problem still lies regarding dssp
Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermediate files are prepared for some time, but I never got any .xpm files, I can not understand whether my system is not working, or I am making any mistake, but all the other programs of Gromacs like pdb2gmx, editconf , genbox, grompp, mdrun etc are going on successfully, problem lies only in case of dssp, I was suggested by Mark to try dssp independently on a single snapshot extracted from the trajectory, I took the snapshot of the protein after 500ps with the command trjconv -f md.xtc -s md.tpr -o time_500ps.pdb -dump 500 (I think the command is correct, if not I earnestly request you to rectify my mistake), When I ran do_dssp on this single structure I waited for 3 days, but it did not finish and seems to be neverending, then I killed the program, In order to get that particular coloured plot of secondary structure vs time which method should I adopt? Seeking your help and thanks in advance. regards SANGEETA - Heres a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] why protein comes out of the box
THANKS A LOT TO ERIK AND MARK regards SANGEETA Mark Abraham <[EMAIL PROTECTED]> wrote: sangeeta kundu wrote: > *Dear Sir,* > ** > * I am facing one problem, I gave the MD run of a protein of > approximately 70 residues for 10ns, after 1 ns run part of protein > was getting out of the waterbox and at the end of 10 ns I found that > almost half of the protein was coming out of the waterbox, I gave the > simulation under NPT condition at 46C and 1BAR pressure, I used 43a1 > force field and spc water.* The protein can't come out of the box... the box is periodic. The protein can *look* like it's come out of the box if your visualization software doesn't know that the system is periodic. > *I used the 43a1 force field, and prepared the water box by the commands * > *editconf -bt triclinic -f conf.pdb -o box.pdb -c -d 1.0 * > *genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top* > ** > *But I wonder that while executing the command* > *grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr* > > *it did not display any charge , Okay, take a step back here. If you didn't know whether the protein should be charged before reaching this point of the system setup, then you haven't stopped to consider whether your simulation is actually modeling anything close to a real physical system. What ionization state do you expect for the ionizable residues? If you put garbage into an MD simulation you get computationally expensive garbage out... > so I did not add any counterion to my > protein, in the subsequent steps em.pdb and pr.mdp files were produced > and in both the cases the protein was almost in the centre of the box, > while I took the snapshot after 1ns the protein was still at the centre > , but after 1 ns it was coming to one corner of the box, and finally > almost half of it was outside the box when I completed the run, I can > not detect why it is coming outside the box?* It's not, but the trajectory is written without attention to the periodicity, since mdrun doesn't know in advance that you plan to visualize and it would be convenient if a particular molecule was always at the center of the simulation box, and you can always reconstruct the "correct" images later (and it would be inefficient for you to tell mdrun in advance). If you do care, you can use the options to trjconv to choose something sensible. See the man pages. > *Where am I doing mistake? Another question is how can I understand that > the simulation has been completed successfully?* First, you need to know what you are hoping to learn from the simulation... Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Heres a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] why protein comes out of the box
Dear Sir, Thanks for your prompt reply, It seems that we do not have to bother about whether the protein is coming out of the box or not as already we introduced pbc? Then how should we understand that the simulation is correct? Will you please kindly check over my md.mdp file, Another trouble I was facing that when running grompp it did not give any information about charge, previously when I ran the same for other proteins it always gave information about charge, so I had to add counter ion , but here I did not. Am I doing any mistake? Please help. regards SANGEETA Erik Marklund <[EMAIL PROTECTED]> wrote: 7 feb 2007 kl. 12.48 skrev sangeeta kundu: Dear Sir, I am facing one problem, I gave the MD run of a protein of approximately 70 residues for 10ns, after 1 ns run part of protein was getting out of the waterbox and at the end of 10 ns I found that almost half of the protein was coming out of the waterbox, I gave the simulation under NPT condition at 46C and 1BAR pressure, I used 43a1 force field and spc water. Why would this be a problem? Proteins do diffuse you know. And since you have pbc the protein cannot really leave the waterbox. /Erik This is my md.mdp file title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 500 ; total 10 ns. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL tau_t = 0.1 0.1 ref_t = 319 319 ; Energy monitoring energygrps = Protein SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 319.0 gen_seed= 173529 I used the 43a1 force field, and prepared the water box by the commands editconf -bt triclinic -f conf.pdb -o box.pdb -c -d 1.0 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top But I wonder that while executing the command grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr it did not display any charge , so I did not add any counterion to my protein, in the subsequent steps em.pdb and pr.mdp files were produced and in both the cases the protein was almost in the centre of the box, while I took the snapshot after 1ns the protein was still at the centre , but after 1 ns it was coming to one corner of the box, and finally almost half of it was outside the box when I completed the run, I can not detect why it is coming outside the box? Where am I doing mistake? Another question is how can I understand that the simulation has been completed successfully? Please help. regards SANGEETA - Heres a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Heres a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] why protein comes out of the box
Dear Sir, I am facing one problem, I gave the MD run of a protein of approximately 70 residues for 10ns, after 1 ns run part of protein was getting out of the waterbox and at the end of 10 ns I found that almost half of the protein was coming out of the waterbox, I gave the simulation under NPT condition at 46C and 1BAR pressure, I used 43a1 force field and spc water. This is my md.mdp file title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 500 ; total 10 ns. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL tau_t = 0.1 0.1 ref_t = 319 319 ; Energy monitoring energygrps = Protein SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 319.0 gen_seed= 173529 I used the 43a1 force field, and prepared the water box by the commands editconf -bt triclinic -f conf.pdb -o box.pdb -c -d 1.0 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top But I wonder that while executing the command grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr it did not display any charge , so I did not add any counterion to my protein, in the subsequent steps em.pdb and pr.mdp files were produced and in both the cases the protein was almost in the centre of the box, while I took the snapshot after 1ns the protein was still at the centre , but after 1 ns it was coming to one corner of the box, and finally almost half of it was outside the box when I completed the run, I can not detect why it is coming outside the box? Where am I doing mistake? Another question is how can I understand that the simulation has been completed successfully? Please help. regards SANGEETA - Heres a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding do_dssp
Thanks for your suggestion. regards Sangeeta On Wed, 07 Feb 2007 18:17:07 +0800, Yang Ye wrote > do_dssp calls external dssp program to do the calculation which is > slow but shall not take "lot of time" . For fast execution of DSSP, > you may consider using my_dssp. > > Go to your gromacs source directory: > ./configure > make > cd src/contrib > make my_dssp > > Regards, > Yang Ye > > On 2/7/2007 5:41 PM, sangeeta wrote: > > Dear Mark, > > > >Previously you suggested to try running dssp independently on a single > > snapshot extracted from the trajectory,I took the snapshot of the protein > > after 1ns with the command > > > > trjconv -f md.xtc -s md.tpr -o time_1000ps.pdb -dump 1000 > > > > then ran dssp program by using the command > > > > dsspcmbi time_1000ps.pdb DSSPtime_1000ps.pdb > > > > The program ran successfully,but again when I used > > > > do_dssp -s md.tpr -f time_1000ps.pdb > > > > the program is taking lot of time.I do not understand where I am making the > > mistake, please help and give me solution.Thanks in advance. > > > > > > regards > > SANGEEA > > > > On Mon, 5 Feb 2007 18:56:22 +1100 (EST), Mark Abraham wrote > > > >>> Dear All, > >>> > >>>I want to analyze the secondary structure of a protein after a > >>> > > 10ns > > > >>> simulation run. Previously I faced difficulty in running dssp program,So > >>> in > >>> order to give a test run I ran the do_dssp program for 100ps > >>> trajectory > >>> only for a protein containing 130 residues.The program continued for > >>> > > more > > > >>> than 4 days, yet it was not completed, Only it was giving the > >>> > > intermediate > > > >>> files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I > >>> do > >>> not understand how long it will take or whether I am encountering any > >>> problem , in the manual it is mentioned that the program is very slow, > >>> But > >>> I am not getting any idea whether the time it is taking is normal, or I > >>> am > >>> facing some problem. > >>> > >> Try doing it on one structure in a trajectory by using trjconv > >> appropriately. If it's not done in ten minutes on a machine under > >> five years old, then you have a problem. > >> > >> Also try running dssp independently on a single snapshot extracted from > >> your trajeotry and put into pdb format (by specifying .pdb suffix on > >> output file for trjconv). If you can't do that, then the problem has > >> nothing to do with gromacs. > >> > >> Mark > >> > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > > > -- > > Open WebMail Project (http://openwebmail.org) > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding do_dssp
Thanks for your suggestion. regards Sangeeta On Wed, 07 Feb 2007 18:17:07 +0800, Yang Ye wrote > do_dssp calls external dssp program to do the calculation which is > slow but shall not take "lot of time" . For fast execution of DSSP, > you may consider using my_dssp. > > Go to your gromacs source directory: > ./configure > make > cd src/contrib > make my_dssp > > Regards, > Yang Ye > > On 2/7/2007 5:41 PM, sangeeta wrote: > > Dear Mark, > > > >Previously you suggested to try running dssp independently on a single > > snapshot extracted from the trajectory,I took the snapshot of the protein > > after 1ns with the command > > > > trjconv -f md.xtc -s md.tpr -o time_1000ps.pdb -dump 1000 > > > > then ran dssp program by using the command > > > > dsspcmbi time_1000ps.pdb DSSPtime_1000ps.pdb > > > > The program ran successfully,but again when I used > > > > do_dssp -s md.tpr -f time_1000ps.pdb > > > > the program is taking lot of time.I do not understand where I am making the > > mistake, please help and give me solution.Thanks in advance. > > > > > > regards > > SANGEEA > > > > On Mon, 5 Feb 2007 18:56:22 +1100 (EST), Mark Abraham wrote > > > >>> Dear All, > >>> > >>>I want to analyze the secondary structure of a protein after a > >>> > > 10ns > > > >>> simulation run. Previously I faced difficulty in running dssp program,So > >>> in > >>> order to give a test run I ran the do_dssp program for 100ps > >>> trajectory > >>> only for a protein containing 130 residues.The program continued for > >>> > > more > > > >>> than 4 days, yet it was not completed, Only it was giving the > >>> > > intermediate > > > >>> files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I > >>> do > >>> not understand how long it will take or whether I am encountering any > >>> problem , in the manual it is mentioned that the program is very slow, > >>> But > >>> I am not getting any idea whether the time it is taking is normal, or I > >>> am > >>> facing some problem. > >>> > >> Try doing it on one structure in a trajectory by using trjconv > >> appropriately. If it's not done in ten minutes on a machine under > >> five years old, then you have a problem. > >> > >> Also try running dssp independently on a single snapshot extracted from > >> your trajeotry and put into pdb format (by specifying .pdb suffix on > >> output file for trjconv). If you can't do that, then the problem has > >> nothing to do with gromacs. > >> > >> Mark > >> > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > > > -- > > Open WebMail Project (http://openwebmail.org) > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding do_dssp
Dear Mark, Previously you suggested to try running dssp independently on a single snapshot extracted from the trajectory,I took the snapshot of the protein after 1ns with the command trjconv -f md.xtc -s md.tpr -o time_1000ps.pdb -dump 1000 then ran dssp program by using the command dsspcmbi time_1000ps.pdb DSSPtime_1000ps.pdb The program ran successfully,but again when I used do_dssp -s md.tpr -f time_1000ps.pdb the program is taking lot of time.I do not understand where I am making the mistake, please help and give me solution.Thanks in advance. regards SANGEEA On Mon, 5 Feb 2007 18:56:22 +1100 (EST), Mark Abraham wrote > > > > Dear All, > > > >I want to analyze the secondary structure of a protein after a 10ns > > simulation run. Previously I faced difficulty in running dssp program,So > > in > > order to give a test run I ran the do_dssp program for 100ps > > trajectory > > only for a protein containing 130 residues.The program continued for more > > than 4 days, yet it was not completed, Only it was giving the intermediate > > files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I > > do > > not understand how long it will take or whether I am encountering any > > problem , in the manual it is mentioned that the program is very slow, > > But > > I am not getting any idea whether the time it is taking is normal, or I > > am > > facing some problem. > > Try doing it on one structure in a trajectory by using trjconv > appropriately. If it's not done in ten minutes on a machine under > five years old, then you have a problem. > > Also try running dssp independently on a single snapshot extracted from > your trajeotry and put into pdb format (by specifying .pdb suffix on > output file for trjconv). If you can't do that, then the problem has > nothing to do with gromacs. > > Mark > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding do_dssp
Dear Mark, Previously you suggested to try running dssp independently on a single snapshot extracted from the trajectory,I took the snapshot of the protein after 1ns with the command trjconv -f md.xtc -s md.tpr -o time_1000ps.pdb -dump 1000 then ran dssp program by using the command dsspcmbi time_1000ps.pdb DSSPtime_1000ps.pdb The program ran successfully,but again when I used do_dssp -s md.tpr -f time_1000ps.pdb the program is taking lot of time.I do not understand where I am making the mistake, please help and give me solution.Thanks in advance. regards SANGEEA On Mon, 5 Feb 2007 18:56:22 +1100 (EST), Mark Abraham wrote > > > > Dear All, > > > >I want to analyze the secondary structure of a protein after a 10ns > > simulation run. Previously I faced difficulty in running dssp program,So > > in > > order to give a test run I ran the do_dssp program for 100ps > > trajectory > > only for a protein containing 130 residues.The program continued for more > > than 4 days, yet it was not completed, Only it was giving the intermediate > > files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I > > do > > not understand how long it will take or whether I am encountering any > > problem , in the manual it is mentioned that the program is very slow, > > But > > I am not getting any idea whether the time it is taking is normal, or I > > am > > facing some problem. > > Try doing it on one structure in a trajectory by using trjconv > appropriately. If it's not done in ten minutes on a machine under > five years old, then you have a problem. > > Also try running dssp independently on a single snapshot extracted from > your trajeotry and put into pdb format (by specifying .pdb suffix on > output file for trjconv). If you can't do that, then the problem has > nothing to do with gromacs. > > Mark > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem regarding do_dssp
Dear All, I want to analyze the secondary structure of a protein after a 10ns simulation run. Previously I faced difficulty in running dssp program,So in order to give a test run I ran the do_dssp program for 100ps trajectory only for a protein containing 130 residues.The program continued for more than 4 days, yet it was not completed, Only it was giving the intermediate files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I do not understand how long it will take or whether I am encountering any problem , in the manual it is mentioned that the program is very slow, But I am not getting any idea whether the time it is taking is normal, or I am facing some problem. Please help, I need your help urgently.Thanks in advance. regards Sangeeta Junior Research Fellow BOSE INSTITUTE KOLKATA,INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] N/A
Dear All, I apologize to all of you because my sent messeges are repeated for more than once because of some server problem, I do not know whether you also are facing the same sort of problem, because I am getting my messege for more than 4 times, So please ignore the messege if it is repeated, I am sorry for this unwanted error. Hope you can understand. regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] N/A
Dear All, I apologize to all of you because my sent messeges are repeated for more than once because of some server problem, I do not know whether you also are facing the same sort of problem, because I am getting my messege for more than 4 times, So please ignore the messege if it is repeated, I am sorry for this unwanted error. Hope you can understand. regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query about protein contact map and salt concentration
Dear All, Is there any option in Gromacs to produce protein contact map? If possible will you please give me some hints? I have seen that other MD programs like CHARMM and AMBER can produce it, so I think certainly GROMACS can do the same.Please help about this matter. Another query is how can I impose salt concentration in my simulation? regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding dssp
Dear Tsjerk, I am sorry I cannot give you the output produced right at the moment when the command "do_dssp -s md.tpr -f traj.xtc." was issued, as far as I remember for that particular program Gromacs was not producing any informative text, as it does in case of other programs, At this moment I do not have the opportunity to access that program due to some internal error,so at this very moment I can not reproduce the result.I can assure you that next time I will definitely report you about the output if it produces any, and I hope you will help. regards SANGEETA On Thu, 25 Jan 2007 13:32:26 +0100, Tsjerk Wassenaar wrote > Hi Sangeeta, > > My request was actually for the text which do_dssp output to the > screen. At this point I do not intend to try to reproduce your error, > and the intermediate files will not prove useful anyway. Running any > of the gromacs programs gives plenty of informative text thrown out > to the screen, in particular when things go wrong. I'm sorry if I haven't > been clear enough there. > > Tsjerk > > On 1/25/07, sangeeta <[EMAIL PROTECTED]> wrote: > > > > Dear Tsjerk, > > > > Previously I send you the intermediate files which are the output of > > DSSP,as per your request, I think I should submit the input files also, so > > here I am attaching the .mdp and .xtc files, the command I used was > > do_dssp -s md.tpr -f traj.xtc.I want to get the particular type of plot of > > secondary structural elements over time as stated in the manual.I > > downloaded DSSP from the link > > > > http://swift.cmbi.ru.nl/gv/dssp/ > > and according to the instruction unpacked by using the command "unzip > > dsspcmbi.zip ", the dssp program by itself ran successfully with the typed > > command > > > > "dsspcmbi PDBSourcefile DSSPDestinationfile ", and I could view the > > destination file with all the structural informations. But when I tried to > > correlate with Gromacs by using "do_dssp -s md.tpr -f traj.xtc" the > > intermediate files are only produced.I understand that something is going > > wrong but can not detect it, please help.Thanks in advence. > > > > regards > > Sangeeta Kundu > > Junior Research Fellow > > Bose Institute, Kolkata > > India > > > > -- > > Open WebMail Project (http://openwebmail.org) > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > 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 don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding dssp
Dear Tsjerk, I am sorry I cannot give you the output produced right at the moment when the command "do_dssp -s md.tpr -f traj.xtc." was issued, as far as I remember for that particular program Gromacs was not producing any informative text, as it does in case of other programs, At this moment I do not have the opportunity to access that program due to some internal error,so at this very moment I can not reproduce the result.I can assure you that next time I will definitely report you about the output if it produces any, and I hope you will help. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding dssp
Dear Tsjerk, I am sorry I cannot give you the output produced right at the moment when the command "do_dssp -s md.tpr -f traj.xtc." was issued, as far as I remember for that particular program Gromacs was not producing any informative text, as it does in case of other programs, At this moment I do not have the opportunity to access that program due to some internal error,so at this very moment I can not reproduce the result.I can assure you that next time I will definitely report you about the output if it produces any, and I hope you will help. regards SANGEETA On Thu, 25 Jan 2007 13:32:26 +0100, Tsjerk Wassenaar wrote > Hi Sangeeta, > > My request was actually for the text which do_dssp output to the > screen. At this point I do not intend to try to reproduce your error, > and the intermediate files will not prove useful anyway. Running any > of the gromacs programs gives plenty of informative text thrown out > to the screen, in particular when things go wrong. I'm sorry if I haven't > been clear enough there. > > Tsjerk > > On 1/25/07, sangeeta <[EMAIL PROTECTED]> wrote: > > > > Dear Tsjerk, > > > > Previously I send you the intermediate files which are the output of > > DSSP,as per your request, I think I should submit the input files also, so > > here I am attaching the .mdp and .xtc files, the command I used was > > do_dssp -s md.tpr -f traj.xtc.I want to get the particular type of plot of > > secondary structural elements over time as stated in the manual.I > > downloaded DSSP from the link > > > > http://swift.cmbi.ru.nl/gv/dssp/ > > and according to the instruction unpacked by using the command "unzip > > dsspcmbi.zip ", the dssp program by itself ran successfully with the typed > > command > > > > "dsspcmbi PDBSourcefile DSSPDestinationfile ", and I could view the > > destination file with all the structural informations. But when I tried to > > correlate with Gromacs by using "do_dssp -s md.tpr -f traj.xtc" the > > intermediate files are only produced.I understand that something is going > > wrong but can not detect it, please help.Thanks in advence. > > > > regards > > Sangeeta Kundu > > Junior Research Fellow > > Bose Institute, Kolkata > > India > > > > -- > > Open WebMail Project (http://openwebmail.org) > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > 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 don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding dssp
Dear Tsjerk, I am sorry I cannot give you the output produced right at the moment when the command "do_dssp -s md.tpr -f traj.xtc." was issued, as far as I remember for that particular program Gromacs was not producing any informative text, as it does in case of other programs, At this moment I do not have the opportunity to access that program due to some internal error,so at this very moment I can not reproduce the result.I can assure you that next time I will definitely report you about the output if it produces any, and I hope you will help. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding dssp
Dear Tsjerk, I am sorry I cannot give you the output produced right at the moment when the command "do_dssp -s md.tpr -f traj.xtc." was issued, as far as I remember for that particular program Gromacs was not producing any informative text, as it does in case of other programs, At this moment I do not have the opportunity to access that program due to some internal error,so at this very moment I can not reproduce the result.I can assure you that next time I will definitely report you about the output if it produces any, and I hope you will help. regards SANGEETA On Thu, 25 Jan 2007 13:32:26 +0100, Tsjerk Wassenaar wrote > Hi Sangeeta, > > My request was actually for the text which do_dssp output to the > screen. At this point I do not intend to try to reproduce your error, > and the intermediate files will not prove useful anyway. Running any > of the gromacs programs gives plenty of informative text thrown out > to the screen, in particular when things go wrong. I'm sorry if I haven't > been clear enough there. > > Tsjerk > > On 1/25/07, sangeeta <[EMAIL PROTECTED]> wrote: > > > > Dear Tsjerk, > > > > Previously I send you the intermediate files which are the output of > > DSSP,as per your request, I think I should submit the input files also, so > > here I am attaching the .mdp and .xtc files, the command I used was > > do_dssp -s md.tpr -f traj.xtc.I want to get the particular type of plot of > > secondary structural elements over time as stated in the manual.I > > downloaded DSSP from the link > > > > http://swift.cmbi.ru.nl/gv/dssp/ > > and according to the instruction unpacked by using the command "unzip > > dsspcmbi.zip ", the dssp program by itself ran successfully with the typed > > command > > > > "dsspcmbi PDBSourcefile DSSPDestinationfile ", and I could view the > > destination file with all the structural informations. But when I tried to > > correlate with Gromacs by using "do_dssp -s md.tpr -f traj.xtc" the > > intermediate files are only produced.I understand that something is going > > wrong but can not detect it, please help.Thanks in advence. > > > > regards > > Sangeeta Kundu > > Junior Research Fellow > > Bose Institute, Kolkata > > India > > > > -- > > Open WebMail Project (http://openwebmail.org) > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > 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 don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem regarding dssp
Dear Tsjerk, Previously I send you the intermediate files which are the output of DSSP,as per your request, I think I should submit the input files also, so here I am attaching the .mdp and .xtc files, the command I used was do_dssp -s md.tpr -f traj.xtc.I want to get the particular type of plot of secondary structural elements over time as stated in the manual.I downloaded DSSP from the link http://swift.cmbi.ru.nl/gv/dssp/ and according to the instruction unpacked by using the command "unzip dsspcmbi.zip ", the dssp program by itself ran successfully with the typed command "dsspcmbi PDBSourcefile DSSPDestinationfile ", and I could view the destination file with all the structural informations. But when I tried to correlate with Gromacs by using "do_dssp -s md.tpr -f traj.xtc" the intermediate files are only produced.I understand that something is going wrong but can not detect it, please help.Thanks in advence. regards Sangeeta Kundu Junior Research Fellow Bose Institute, Kolkata India -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem regarding dssp
dear Sir, Thanks a lot for your reply.I am sorry for the fact that my subject name does not tally with the problem I faced.I really apologize for that. So I do not need to include explicitely "pbc=xyz" in my .mdp file as it is already being used by default. Regarding dssp I used the following commands export DSSP=/home/debjani/dssp setenv DSSP /home/debjani/dssp do_dssp -s md.tpr -f traj.xtc At the end of the program only the files namely ddEZ117f ddOWnvlx etc were present, but no .xpm files were there.I want to get the plot of changing of secondary structural elements during the run.PLease help. regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem regarding dssp
dear Sir, Thanks a lot for your reply.I am sorry for the fact that my subject name does not tally with the problem I faced.I really apologize for that. So I do not need to include explicitely "pbc=xyz" in my .mdp file as it is already being used by default. Regarding dssp I used the following commands export DSSP=/home/debjani/dssp setenv DSSP /home/debjani/dssp do_dssp -s md.tpr -f traj.xtc At the end of the program only the files namely ddEZ117f ddOWnvlx etc were present, but no .xpm files were there.I want to get the plot of changing of secondary structural elements during the run.PLease help. regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem regarding dssp
dear Sir, Thanks a lot for your reply.I am sorry for the fact that my subject name does not tally with the problem I faced.I really apologize for that. So I do not need to include explicitely "pbc=xyz" in my .mdp file as it is already being used by default. Regarding dssp I used the following commands export DSSP=/home/debjani/dssp setenv DSSP /home/debjani/dssp do_dssp -s md.tpr -f traj.xtc At the end of the program only the files namely ddEZ117f ddOWnvlx etc were present, but no .xpm files were there.I want to get the plot of changing of secondary structural elements during the run.PLease help. regards Sangeeta On Wed, 24 Jan 2007 09:45:02 +0100, Tsjerk Wassenaar wrote > Hi Sangeeta, > > To start with, you don't really describe a problem regarding pbc, as > you've stated in the subject. Please make the subject reflect your > problem or question directly. This will make it easier on the > repliers on this list to check whether they can be of any help. Most > of us read/discard messages based on the subject. > > Now, you have three questions, which you've stated before, but > apparently the answers were not informative enough. To start with the > pbc, gromacs uses pbc unless explicitly stated otherwise, by adding > pbc=no in the .mdp file. > > Regarding the chlorides, I think you caught that you have to have an > #include statement in the .top file, reading #include "ions.itp". The > next thing to make sure is that the name you've used for your > chloride ions in the .top file matches those in the file ions.itp > listed for the force field you are using. It may be CL, Cl, Cl-. You > can try either or you can check the file ions.itp in your > $GMXDIR/share/gromacs/top directory. > > Finally, regarding dssp, please explain what you tried to do, i.e. > which command you've issued. Note that the file you mentioned is > merely a temporary file. > > Hope it helps, > > Tsjerk > > On 1/24/07, sangeeta <[EMAIL PROTECTED]> wrote: > > > > Dear GROMACS list members, > > > > > >I have three questions, > > > >My protein has +2 charge, so I added two Cl atoms through the program > > genion and subsequently edited the topol.top file, in spite of that while > > running mdrun it gave an error that "FATAL error, CL atom type can not be > > found",I can not understand the problem. > >I wanted to include PBC in my simulation, I want to know that does > > Gromacs by default use the option by minimum image convention or we have to > > edit pr.mdp & md.mdp by writing PBC=xyz ,How can I know that PBC is > > being included in my simulation? > > In spite of having dssp and running it I can not get the .xpm files. > > Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx > > are being produced.How can I generate those xpm files? > > Waiting for your reply. > > > > regards > > SANGEETA > > > > -- > > Open WebMail Project (http://openwebmail.org) > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > 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 don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem regarding pbc
Dear GROMACS list members, I have three questions, My protein has +2 charge, so I added two Cl atoms through the program genion and subsequently edited the topol.top file, in spite of that while running mdrun it gave an error that "FATAL error, CL atom type can not be found",I can not understand the problem. I wanted to include PBC in my simulation, I want to know that does Gromacs by default use the option by minimum image convention or we have to edit pr.mdp & md.mdp by writing PBC=xyz ,How can I know that PBC is being included in my simulation? In spite of having dssp and running it I can not get the .xpm files. Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those xpm files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem regarding pbc
Dear GROMACS list members, I have three questions, My protein has +2 charge, so I added two Cl atoms through the program genion and subsequently edited the topol.top file, in spite of that while running mdrun it gave an error that "FATAL error, CL atom type can not be found",I can not understand the problem. I wanted to include PBC in my simulation, I want to know that does Gromacs by default use the option by minimum image convention or we have to edit pr.mdp & md.mdp by writing PBC=xyz ,How can I know that PBC is being included in my simulation? In spite of having dssp and running it I can not get the .xpm files. Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those xpm files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] N/A
Dear Sir, I have three questions, My protein has +2 charge, so I added two Cl atoms through the program genion and subsequently edited the topol.top file, in spite of that while running mdrun it gave an error that "FATAL error, CL atom type can not be found",I can not understand the problem. I wanted to include PBC in my simulation so in the pr.mdp file as well in md.mdp file I wrote PBC=xyz , am I correct? How can I know that PBC is being included in my simulation? In spite of having dssp and running it I can not get the .xpm files. Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem regarding dssp
Dear Sir, After carrying out one MD simulation of a protein when I went for analysis of secondary structure through dssp the program ran successfully, but no .xpm files were generated.I can not understand the problem , please help. -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] N/A
Dear Sir, I have three questions, My protein has +2 charge, so I added two Cl atoms through the program genion and subsequently edited the topol.top file, in spite of that while running mdrun it gave an error that "FATAL error, CL atom type can not be found",I can not understand the problem. I wanted to include PBC in my simulation so in the pr.mdp file as well in md.mdp file I wrote PBC=xyz , am I correct? How can I know that PBC is being included in my simulation? In spite of having dssp and running it I can not get the .xpm files. How can I generate those files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem regarding xmgr
Dear GROMACS list members, It may be a very trivial question,But I can not solve it, please help,The commands like xmgrace,xpsview,xmgr, my-dssp are not working. How could I get out of that problem? regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] query about protein-ligand complex
I could not mail you as our net was down, you asked me "Is your system properly minimized? " My question is how can I understand whether my system is properly minimised? the run is still going on, I can realize that something is going wrong. But I can not detect it.The log file is giving the error that the system is not properly minimised.I am giving you the messege, "2127 2131 176.6 223178260480. 3921810030592. 0.1330 2128 2129 176.6 69075034112. 1233987043328. 0.1000 2128 2130 176.6 69075394560. 1233986912256. 0.1000 2131 2132 176.5 69056528384. 1233902108672. 0.1000 2131 2133 176.5 69054996480. 1233896734720. 0.1000 Constraint error in algorithm Lincs at step 9 t = 0.018 ps: Water molecule starting at atom 13339 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Large VCM(group rest): -168597.92188, 112023.07031, -175543.56250, ekin-cm: 3.95206e+15 " will you please give me some suggestion , so that I can run the system from the beginning? regards Sangeeta On Fri, 30 Jun 2006 14:50:44 +0200, Erik Marklund wrote > On Fri, 2006-06-30 at 17:52 +0530, sangeeta wrote: > > > > Dear all, > > > > I am trying to run the dynamics of protein-ligand complex following the > > tutorial "GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1" > > . I am running position restricted dynamics of the 91az8.pdb protein as > > mentioned in the tutorial trp.pdb & drg.pdb)in a Linux server machine, I can > > not understand why it is taking such a long time, the machine is not busy > > with any other jobs.I ran it before & I stopped the run at 1200 min, now it > > is going for about 215 min, & step6.pdb, step7.pdb etc files are being > > formed, I can not undersyand whether I am doing any wrong step, why it is > > taking such a long time , I don't know , please help. > > stepX.pdb files are generated when things go wrong, for example when > forces or other quantities becomes NaN or Inf. The log files should give > some clues about what is happening to your system.Is your system > properly minimized? Please provide some more information, otherwise it's > difficult to help you. > > /Erik Marklund > > > > > regards > > sangeeta > > Open WebMail Project (http://openwebmail.org) > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- > Erik Marklund, PhD Student, Molecular Biopcysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4537 fax: 46 18 511 755 > [EMAIL PROTECTED] > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query about protein-ligand complex
Dear all, I am trying to run the dynamics of protein-ligand complex following the tutorial "GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1" . I am running position restricted dynamics of the 91az8.pdb protein as mentioned in the tutorial trp.pdb & drg.pdb)in a Linux server machine, I can not understand why it is taking such a long time, the machine is not busy with any other jobs.I ran it before & I stopped the run at 1200 min, now it is going for about 215 min, & step6.pdb, step7.pdb etc files are being formed, I can not undersyand whether I am doing any wrong step, why it is taking such a long time , I don't know , please help. regards sangeeta Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] N/A
Hi, Can anyone suggest me is it possible to carry a minimisation followed by MD simulation in Groamcs in a water box keeping both the ligand and the substrate fixed?The backbone of the protein will also be fixed. regards SANGEETA KUNDU JUNIOR RESEARCH FELLOW BOSE INSTITUTE KOLKATA -- Open WebMail Project (http://openwebmail.org) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
