[gmx-users] analysis of membrane protein
hi all, i have simulated a membrane protein system in DPPC and DMPC bilayer. i have got the trajectories and analysed them with the gromacs tools. now i want to get the bonding connectivity of the protein with that of the lipid layer. can i get that graphically (i.e. in xvg format) ? is there any option to visualize the protein - lipid connections other than ngmx? as the system is big enough i cant get a clear idea about the bonding patterns of the protein with the lipid bilayerwaiting for suggestions Thank You all Shamik See the Web#39;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] error in Deuterium order analysis
hi all, i am analyzing a trajectory of a membrane protein embedded in DMPC bilayer. for this i'm using deuterium order analysis where i have created two different index groups for the acyl chains. now when i am running g_order its giving an error message like Program g_order, VERSION 4.0.5 Source code file: gmx_order.c, line: 362 Fatal error: grp 1 does not have same number of elements as grp 1 can anybody tell me where this kind of error generating from? and how to solve this problem? is there any problem in the index group creation? a little help would be very encouraging Thanking You all Shamik Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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
Re: [gmx-users] error in Deuterium order analysis
--- On Mon, 31/8/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] error in Deuterium order analysis To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 31 August, 2009, 7:25 PM Samik Bhattacharya wrote: hi all, i am analyzing a trajectory of a membrane protein embedded in DMPC bilayer. for this i'm using deuterium order analysis where i have created two different index groups for the acyl chains. now when i am running g_order its giving an error message like Program g_order, VERSION 4.0.5 Source code file: gmx_order.c, line: 362 Fatal error: grp 1 does not have same number of elements as grp 1 can anybody tell me where this kind of error generating from? and how to solve this problem? is there any problem in the index group creation? a little help would be very encouraging Yes, your index groups are wrong. There is a step-by-step how-to on the wiki: http://oldwiki.gromacs.org/index.php/g_order -Justin Thanking You all Shamik Thanks Justin again for the answar.. Shamik Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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
Re: [gmx-users] problem installing gromacs
--- On Thu, 13/8/09, st y1...@ucsd.edu wrote: From: st y1...@ucsd.edu Subject: [gmx-users] problem installing gromacs To: gmx-users@gromacs.org Date: Thursday, 13 August, 2009, 1:42 AM Hi There, I have some problems installing gromacs on the linux server. fftw installed with no error, but when I install gromacs, I got the following error: * /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/home/y1gao/soft/fftw/lib -o grompp grompp.o libgmxpreprocess_d.la ../mdlib/l cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o .libs/grompp grompp.o -L/home/y1gao/soft/fftw/lib ./.libs/libgmxpreprocess_d.a -L/usr/X11R6/lib ../mdlib/.libs/libmd_d.so /n _d.so -lnsl -lfftw3 -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/home/y1gao/soft/gromacs//lib .../mdlib/.libs/libmd_d.so: undefined reference to `__libm_sse2_sincos' .../mdlib/.libs/libmd_d.so: undefined reference to `__libm_sse2_log' .../mdlib/.libs/libmd_d.so: undefined reference to `_intel_fast_memcpy' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src' make: *** [all-recursive] Error 1 *** I used the combinations of the following fftw and gromacs: fftw 3.2.1; fftw3.2.2 gromacs 3.3.3; gromacs 4.0.4 gcc version 3.4.6 try with make links after make install of gromacs. probably this may help. good luck The command I used are: * To install fftw: $ ./configure --enable-threads --enable-sse2 -prefix /home/y1gao/soft/fftw/lib $ make $ make install To install gromacs: $ ./configure --enable-shared LDFLAGS='-L/home/y1gao/soft/fftw/lib' CPPFLAGS='-I/home/y1gao/soft/fftw/include' --enable-double --prefix=/home/y1gao/soft/gromacs/ $ make $ make install ( error comes out here) * Could anyone help me find a way out? Thanks in advance. Stone -Inline Attachment Follows- ___ gmx-users mailing list gmx-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 Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ 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] analysis of result
hi i have completed the process of simulating a protein in a lipid environmant... now in the analysis part i have generated some graphical representations of the angle, RMSD etc. but from that i cant conclude about the success of the simulation.is there any thing (research papers, namely) whcih can provide ideas about how to reach conclusion from the analysed data.really need some help regarding this matter... Thank You Shamik See the Web#39;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
Re: [gmx-users] analysis of result
--- On Mon, 3/8/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] analysis of result To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 3 August, 2009, 5:03 PM Samik Bhattacharya wrote: hi i have completed the process of simulating a protein in a lipid environmant... now in the analysis part i have generated some graphical representations of the angle, RMSD etc. but from that i cant conclude about the success of the simulation.is there any thing (research papers, namely) whcih can provide ideas about how to reach conclusion from the analysed data..really need some help regarding this matter Everyone's conclusions are going to be different based on the question they are trying to answer. The necessary analysis should be derived from this question. Such decisions should be made before running the MD :) -Justin Thank You Shamik first of all thanks a lot Justin for your reply.obviously i agree with you. i want to study the activity of some membrane proteins in different environments. for that i just want to know which parameters i need to consider. things which are common has already been analyzed...i just need some references to make sure i'm not missing any details which could lead me to any other conclusion... waiting for you reply.. Thanks a lot for your time and really helpful suggestions Shamik Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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
Re: [gmx-users] analysis of result
--- On Mon, 3/8/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] analysis of result To: Gromacs Users' List gmx-users@gromacs.org Date: Monday, 3 August, 2009, 8:23 PM Samik Bhattacharya wrote: --- On *Mon, 3/8/09, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] analysis of result To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 3 August, 2009, 5:03 PM Samik Bhattacharya wrote: hi i have completed the process of simulating a protein in a lipid environmant... now in the analysis part i have generated some graphical representations of the angle, RMSD etc. but from that i cant conclude about the success of the simulation.is there any thing (research papers, namely) whcih can provide ideas about how to reach conclusion from the analysed data.really need some help regarding this matter Everyone's conclusions are going to be different based on the question they are trying to answer. The necessary analysis should be derived from this question. Such decisions should be made before running the MD :) -Justin Thank You Shamik first of all thanks a lot Justin for your reply.obviously i agree with you. i want to study the activity of some membrane proteins in different environments. for that i just want to know which parameters i need to consider. things which are common has already been analyzedi just need some references to make sure i'm not missing any details which could lead me to any other conclusion... A simple literature search will turn up dozens (if not hundreds) of useful papers related to membrane protein MD. There are not necessarily any universal parameters that should be analyzed - if your study is about activity of a membrane protein, is lateral diffusion of lipids important? If the answer is no, then you've wasted your time running the analysis and searching for papers about it :) -Justin waiting for you reply.. Thanks a lot for your time and really helpful suggestions Shamik ok, thank you Justini got what you meant to say thanks you for the help... Shamik Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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] GHrace install
hi alli'm facing alot of trouble in installing grace in my redhat machine. its always complaining about Motiff API. ive installed Lesstiff but even afetr that grace is not getting installed...i can't make out how to install it? is there any problem in the path? should i've to set path before grace install. i've gone through several pages about grace installation but with no effect.ac anyone pls tell me how to install Grace in Fedora of Redhat? thanking you all Shamik See the Web#39;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
Re: [gmx-users] POSITION-RESTRAIN
--- On Mon, 27/7/09, Morteza Khabiri khab...@greentech.cz wrote: From: Morteza Khabiri khab...@greentech.cz Subject: [gmx-users] POSITION-RESTRAIN To: gmx-users@gromacs.org Date: Monday, 27 July, 2009, 7:35 PM Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I found the similar error in the mailing list and they suggested probably the place of restraint itp file which was included in topology file is wrong. However, I tried several positions for restraint itp but I think it is not the solution. Do you have any other suggestion about this problem?? Thanks hi, Mark is right.the position restrain.itp file should be included in your topology file in the proper place otherwise the problem would continue. place the .itp file after the section ; Include Position restraint file #ifdef POSRES #include posre.itp #endif best wishes Shamik ___ gmx-users mailing list gmx-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 Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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] large force on an atom
hi, i'm simulating a membrane protein in DPPC bilayer. here i'm using inflategro perl script. just after the first run when i'm running grompp to minimize it i have found a large force on a phenylalanin atom which is well over 1015 Now what to do with this one? I had a view of that particular atom through pymol which is an Oxygen (CO). Right now I’m a little anxious that if I keep this and go on it’ll affect the future steps. Any suggestions regarding this will be very encouraging. Thank You Shamik Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ 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] installing grace
hi, i am simulating a peptide in lipid bilayer where i've completed the production run. but the problem is that i cant install grace as it requires motiff api. a have installed lesstiff but still when i am going to intall grace its again complaining theat it could not find motiff api. it'll be great to have some suggestions regarding grace and motiff installtion. i am using a red hat enterprise edition linux machine. is there any other software than gace to plot the generated graphical output? Thaking you Shamik Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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] Lincs Warning
Hi all, i ma simulating a membrane protein, in which i am facing a problem in the equilibration step. in the NVT equilibration when i am running the mdrun command i am getting a msg like Program mdrun, VERSION 4.0.5 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1966) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem i cant understand how to fix the problem. where actually lies the error? is it in the mdp file i am using? some suggestions will be really helpful in this regard. Thank you all for the help in advance. Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Lincs Warning
--- On Wed, 15/7/09, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Lincs Warning To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 15 July, 2009, 5:23 PM Samik Bhattacharya wrote: Hi all, i ma simulating a membrane protein, in which i am facing a problem in the equilibration step. in the NVT equilibration when i am running the mdrun command i am getting a msg like Program mdrun, VERSION 4.0.5 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1966) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem i cant understand how to fix the problem. where actually lies the error? is it in the mdp file i am using? some suggestions will be really helpful in this regard. Thank you all for the help in advance. http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings Thanks You Mark. for your help... perhaps the error lies lies in EM step which converged very early in previous steps. when i was running EM for 5000 steps it was converging in less than 50 steps. and was showing a msg like Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision would doule precision remove this problem? again i cant rule out the system blowing up error. in that case how to increase 1-4 interaction? looking forward for your valuable comments. Thank You Shamik Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Lincs Warning
--- On Thu, 16/7/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Lincs Warning To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, 16 July, 2009, 7:30 AM Samik Bhattacharya wrote: --- On *Wed, 15/7/09, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Lincs Warning To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 15 July, 2009, 5:23 PM Samik Bhattacharya wrote: Hi all, i ma simulating a membrane protein, in which i am facing a problem in the equilibration step. in the NVT equilibration when i am running the mdrun command i am getting a msg like Program mdrun, VERSION 4.0.5 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1966) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem i cant understand how to fix the problem.. where actually lies the error? is it in the mdp file i am using? some suggestions will be really helpful in this regard. Thank you all for the help in advance. http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings Thanks You Mark. for your help... perhaps the error lies lies in EM step which converged very early in previous steps. when i was running EM for 5000 steps it was converging in less than 50 steps. and was showing a msg like Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision would doule precision remove this problem? again i cant rule out the system blowing up error. in that case how to increase 1-4 interaction? looking forward for your valuable comments. Thank You Shamik The question is not when energy minimization converged, but whether or not it converged to an appropriate value of Epot and Fmax. What values did you obtain? -Justin hi, Justin..good to hear from you again... the values i got are given below (taken from the log file): Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 31 steps, but did not reach the requested Fmax 1000. Potential Energy = -1.0261834e+23 Maximum force = 4.9815813e+24 on atom 169274 Norm of force = 6.4473938e+21 M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops --- LJ 30.494607 1006.322 0.1 Coul(T) 24.286588 1020.037 0.1 Coul(T) [W3] 0.205871 25.734 0.0 Coul(T) + LJ 13.019726 716.085 0.0 Coul(T) + LJ [W3] 8.396028 1158.652 0.1 Coul(T) + LJ [W3-W3] 3018.437056 1153042.955 71.1 Outer nonbonded loop 318.129558 3181.296 0.2 1,4 nonbonded interactions 0.204724 18.425 0.0 Calc Weights 229.781517 8272.135 0.5 Spread Q Bspline 4902.005696 9804.011 0.6 Gather F Bspline 4902.005696 58824.068 3.6 3D-FFT 21969.184718 175753.478 10.8 Solve PME 234.707200 15021.261 0.9 NS-Pairs 8380.302391 175986.350 10.8 Reset In Box 25.604636 76.814 0.0 Shift-X 76.593746 459.562 0.0 CG-CoM 76.593839 229.782 0.0 Bonds 0.247597 14.608 0.0 Angles 0.306280 51.455 0..0 Propers 0.117800 26.976 0..0 Impropers 0.043276 9.001 0.0 RB-Dihedrals 0.092256 22.787 0.0 Virial 76.595234 1378.714 0.1 Settle 50.895614 16439.283 1.0 --- Total
[gmx-users] MdRun Crash
hi, I am running a simulation of a membrane protein in DPPC bilayer. ii have completed upto genion step. But when i am going to minimize the energy of the system the mdrun crashes showing Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -9.8290938e+21 Maximum force = 6.7779973e+24 on atom 5591 Norm of force = 2.4384918e+22 i can understand the problem lies in the mdp file used, i.e. in the Epot and Fmax. i have rerun the step using different values but with same result.please suggest me how to overcome the constraints problem. thanking you in advance. mdp file is here integrator = steep emstep = 0.001 emtol = 1000 nsteps = 5000 nstlist = 1 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 pbc = xyz Shamik Looking for local information? Find it on Yahoo! Local http://in.local.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] waters in ion channels
hi i'm simulating a ion channel protein in DPPC membrane. i'm following Justin's tutorial for that. and have completed upto the solvation step. but right after solvation, i found some water molecules in the channel. now i want to delete those molecules. in the tutorial it is advised tyo use the keepbyz script to do that.. but after using that i didn't find any change in the structure. watres are still present in there. may be i am making some mistake in running the program or something like that!!! can anyone suggest any thing to solve the problem...thanking you all in advance. Looking for local information? Find it on Yahoo! Local http://in.local.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
Re: [gmx-users] waters in ion channels
--- On Fri, 3/7/09, Itamar Kass itamar.k...@gmail.com wrote: From: Itamar Kass itamar.k...@gmail.com Subject: Re: [gmx-users] waters in ion channels To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 3 July, 2009, 3:42 PM Hi, I would say that those are water molecule which enter from the bulk water. This is normal and probably important for the physiological function of the system. Best, Itamar thank you a lot for the answar. one thing i would like to ask again that how can i be sure that those water molecules are not inside the hydrophobic core? and if they are not how deleting them could affect the system? thanks again Shamik On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharyasamikb...@yahoo.co.in wrote: hi i'm simulating a ion channel protein in DPPC membrane. i'm following Justin's tutorial for that. and have completed upto the solvation step. but right after solvation, i found some water molecules in the channel. now i want to delete those molecules. in the tutorial it is advised tyo use the keepbyz script to do that.. but after using that i didn't find any change in the structure. watres are still present in there. may be i am making some mistake in running the program or something like that!!! can anyone suggest any thing to solve the problem...thanking you all in advance. Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. ___ 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 mailing list gmx-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 Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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] problem in grompp -broken charge
hi, Justin, i have completed upto the genion step of that simulation. One error is creeping in this step which is nonzero system charge. my system is said to have a charge 1.69. now how to neutralize this kind of broken charge? another thing is that how this kind of broken chage is being developed? i think something was wrong in previous steps. but can't recognise which step to account for this anomalous behavior? waiting for your valuable suggestions... Thanks again.. Shamik Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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] problem in running grompp
hi, i am simulating a membrane protein inside dppc bilayer and in this regard i am following justin's tutorial. but i ma facing a problem in running grompp...whenever i run it is giving error Program grompp, VERSION 4.0.5 Source code file: grompp.c, line: 362 Fatal error: number of coordinates in coordinate file (1A68_genbox.gro, 49128) does not match topology (1A68.top, 48628) now how to solve this problem? i have first generated the lipid box with the protein then solvated it. i really need little bit of help to proceed to the next step... Thaking You... Shamik Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.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
Re: [gmx-users] problem in running grompp
--- On Mon, 8/6/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] problem in running grompp To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 8 June, 2009, 4:47 PM Samik Bhattacharya wrote: hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is generting an error as follows ''Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 843 Fatal error: Atomtype CA not found'' but is not CA the main chain alpha carbon...why is not grompp taking CA then? i can't make out where the problem lies? i little help on this shall be very encouraging. If you're seeing this error, then you've done something wrong when combining lipid.itp with the Gromos force field file. -Justin Thank You Shamik Thank you Justin for the answar. but now how to solve it? where should i make changes to correct that? pls let me know what to do... waiting for your answar Thank you again.. ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-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 Own a website.Get an unlimited package.Pay next to nothing.*Go to http://in.business.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] problem in running grompp
hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is generting an error as follows ''Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 843 Fatal error: Atomtype CA not found'' but is not CA the main chain alpha carbon...why is not grompp taking CA then? i can't make out where the problem lies? i little help on this shall be very encouraging. Thank You Shamik Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.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] installation
hi,I i am facing a lot of troubles in installing Gromacs in my Redhat machine..I've followed all the instructions given in the manual as well as in the website. ialso have installed fftw,its compiling with no problem. . but whenever i run pdb2gmx or command lke that its giving an error command not found. a little help regarding this matter will be very encouraging. thankx Shamik Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/___ 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] membrane protein simulation
hi i'm new to gromacs and want to simulate a protein inside a phospholipid envelop (may be box or dodecahedron). for this i got the pdb files of both the proteins and the lipids(e.g.POPC, POPE etc). but i'm facing a lot of problems in generating the topology files as well as in running grompp as gromacs does not support lipids. i also tested it by using the lipid.itp file in the top directory. can anyone suggest me any tutorial where i can find detailed discussion on this matter? and obviously some help in how to go for it?? Thanking you in advance Shamik Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] membrane protein simulation
Thanx Justin...i must go throuh that tutorial. thanx for the help. --- On Fri, 29/5/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] membrane protein simulation To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 29 May, 2009, 4:49 PM Samik Bhattacharya wrote: hi i'm new to gromacs and want to simulate a protein inside a phospholipid envelop (may be box or dodecahedron). for this i got the pdb files of both the proteins and the lipids(e.g.POPC, POPE etc). but i'm facing a lot of problems in generating the topology files as well as in running grompp as gromacs does not support lipids. i also tested it by using the lipid.itp file in the top directory. can anyone suggest me any tutorial where i can find detailed discussion on this matter? and obviously some help in how to go for it?? Yes, there is a tutorial here: http://wiki.gromacs.org/index.php/Membrane_Simulations#Running_Membrane_Simulations -Justin Thanking you in advance Shamik Own a website.Get an unlimited package.Pay next to nothing.* Click here!. http://in.rd.yahoo.com/tagline_ysb_website/*http://in.business.yahoo.com/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-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 Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/___ 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] simulation of protein in popc box
hi i am new to Gromacs. i want to simulate a protein inside a lipid box(preferably POPC or POPE). i have generated the protein inside the POPC box complex. But whenever i am going to build the .gro and .top file of that complex with pdb2gmx an error is creeping in saying Cant find POP in residue topology database. it cant recognise the lipid.itp and popc.itp files which i've already put into the top directory. plese help me out. thank you Bollywood news, movie reviews, film trailers and more! Go to http://in.movies.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulation of protein in popc box
Thanks pawan, for helping but one problem still remains that is how to incorporate the .itp file inside the topology file and which .itp file should i include is it the lipid.itp orr POPC.itp?? thanx for your help Shamik Greetings from Pawan. Topologies for lipids like POP are not available in the topology database in gromacs. So the starting point would be to generate a topology and a gro file for the protein alone as such and then edit the topology to include the .itp files as specifically needed for the lipids. Regards, Pawan On Fri, May 22, 2009 at 4:42 PM, Samik Bhattacharya samikb...@yahoo.co.in wrote: hi i am new to Gromacs. i want to simulate a protein inside a lipid box(preferably POPC or POPE). i have generated the protein inside the POPC box complex. But whenever i am going to build the .gro and .top file of that complex with pdb2gmx an error is creeping in saying Cant find POP in residue topology database. it cant recognise the lipid.itp and popc.itp files which i've already put into the top directory. plese help me out. thank you Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -Inline Attachment Follows- ___ gmx-users mailing list gmx-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 Bollywood news, movie reviews, film trailers and more! Go to http://in.movies.yahoo.com/___ 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
