Re: [gmx-users] sampling conformation on the basis of RMSD value
Hi, below you can find a dirty perl script that I used to extract A dirty perl script... That's a tautology! :p Of course, to put that remark on the list, I sort of oblige myself to add two cents to the discussion :p I recall that the original question was literally asking to extract the frames which fall below a certain RMSD cut-off from a reference. That's not (necessarily) the same as extracting the members belonging to a certain cluster. There may be several (parts of) clusters meeting the RMSD criterium. If the purpose is to filter based on RMSD prior to a cluster analysis, you would need to extract those frames from the trajectory first. trjconv offers an option -drop for that. This allows reading an .xvg file along with your trajectory and using -dropunder x.y you can select all frames which have a value under the one specified :) Hope it helps. Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] using vmd output for MDRUN
Hi There, Following is the scenario I am trying for MDS I am using vmd to modify the position of my molecule, and then output from vmd is in .pdb format. for .top file I have generated those files from pdb2gmx and edited them manually as suggested in drug-enzyme tutorial by J E Kerrigan. Now, I am in doubt weather I can use the .pdb from vmd .top file for running editconf and genbox followed by MDS ? With Thanks, Vivek ___ 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] topology of cyclohexane
I once built one from the standart opls-atoms. It is ENTIRELY UNTESTED! I have absolutely no clue how good it is. In particular the partial charges on the H and C may have to be improved. best, Jochen Here is also a pdb: TITLE One Cyclohexane REMARKTHIS IS A SIMULATION BOX CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 CA CYC 1 26.075 25.752 1.621 1.00 0.00 ATOM 2 HA1 CYC 1 26.881 25.711 0.887 1.00 0.00 ATOM 3 HA2 CYC 1 25.289 25.092 1.251 1.00 0.00 ATOM 4 CB CYC 1 25.534 27.188 1.727 1.00 0.00 ATOM 5 HB1 CYC 1 25.141 27.510 0.762 1.00 0.00 ATOM 6 HB2 CYC 1 26.351 27.869 1.969 1.00 0.00 ATOM 7 CC CYC 1 24.440 27.294 2.801 1.00 0.00 ATOM 8 HC1 CYC 1 23.568 26.715 2.493 1.00 0.00 ATOM 9 HC2 CYC 1 24.106 28.329 2.891 1.00 0.00 ATOM 10 CD CYC 1 24.941 26.784 4.162 1.00 0.00 ATOM 11 HD1 CYC 1 24.135 26.825 4.896 1.00 0.00 ATOM 12 HD2 CYC 1 25.727 27.444 4.533 1.00 0.00 ATOM 13 CE CYC 1 25.482 25.349 4.056 1.00 0.00 ATOM 14 HE1 CYC 1 24.665 24.668 3.814 1.00 0.00 ATOM 15 HE2 CYC 1 25.875 25.027 5.021 1.00 0.00 ATOM 16 CF CYC 1 26.577 25.242 2.982 1.00 0.00 ATOM 17 HF1 CYC 1 27.448 25.821 3.290 1.00 0.00 ATOM 18 HF2 CYC 1 26.911 24.208 2.892 1.00 0.00 TER ENDMDL Here is the hdb entry. Add it to ffoplsaa.hdb: CYC 6 24 HA CA CB CF 24 HB CB CA CC 24 HC CC CB CD 24 HD CD CC CE 24 HE CE CD CF 24 HF CF CE CA Here is the rtp entry. Add it to ffoplsaa.rtp and run pdb2gmx. ; cyclohexane [ CYC ] [ atoms ] CA opls_136 -0.120 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 CB opls_136 -0.120 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CC opls_136 -0.120 3 HC1 opls_140 0.060 3 HC2 opls_140 0.060 3 CD opls_136 -0.120 4 HD1 opls_140 0.060 4 HD2 opls_140 0.060 4 CE opls_136 -0.120 5 HE1 opls_140 0.060 5 HE2 opls_140 0.060 5 CF opls_136 -0.120 6 HF1 opls_140 0.060 6 HF2 opls_140 0.060 6 [ bonds ] CA HA1 CA HA2 CA CF CA CB CB HB1 CB HB2 CB CC CC HC1 CC HC2 CC CD CD HD1 CD HD2 CD CE CE HE1 CE HE2 CE CF CF HF1 CF HF2 Vitaly Chaban wrote: Guys, Does anybody have an already prepared topology of cyclohexane? Thanks. -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ 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] harmonic restraint
Jae Hyun Park wrote: Dear all GROMACS users, I'm new in protein simulation. Does anybody let me know in what subroutine the harmonic restraint is implemented? If I would like to trace back to the subroutine from md.c, how can I do that? I really appreciate any comments on such a beginner's question. If you mean position restraints, they are in posres() in bondfree.c Best, Jochen Best, Jae H. Park === Jae Hyun Park, Ph.D. Visiting Scholar 3215 Beckamn Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801 (Tel) 217-244-4353, (FAX) 217-244-4333 (E-mail) [EMAIL PROTECTED] ___ 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 . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ 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] GROMACS sample procedure
I am new to GROMACS and have not tried any calculation using it. I have installed grmx on scientific linux. Can anyone help me find a sample procedure of using GROMACS for molecular dynamics simulation (or even for simple energy calculation)? I am interested in doing research on Molecular Dynamics using GROMACS, but so far, I really dont have an idea where to start. I hope to hear your advise. Thank you very much Christopher Ambe MSU-Iligan Institute of Technology ___ 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[2]: [gmx-users] topology of cyclohexane
Jochen, Thank you! Vitaly JH I once built one from the standart opls-atoms. It is ENTIRELY UNTESTED! JH I have absolutely no clue how good it is. In particular the partial JH charges on the H and C may have to be improved. JH best, Jochen JH Here is also a pdb: JH TITLE One Cyclohexane JH REMARKTHIS IS A SIMULATION BOX JH CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1 JH MODEL1 JH ATOM 1 CA CYC 1 26.075 25.752 1.621 1.00 0.00 JH ATOM 2 HA1 CYC 1 26.881 25.711 0.887 1.00 0.00 JH ATOM 3 HA2 CYC 1 25.289 25.092 1.251 1.00 0.00 JH ATOM 4 CB CYC 1 25.534 27.188 1.727 1.00 0.00 JH ATOM 5 HB1 CYC 1 25.141 27.510 0.762 1.00 0.00 JH ATOM 6 HB2 CYC 1 26.351 27.869 1.969 1.00 0.00 JH ATOM 7 CC CYC 1 24.440 27.294 2.801 1.00 0.00 JH ATOM 8 HC1 CYC 1 23.568 26.715 2.493 1.00 0.00 JH ATOM 9 HC2 CYC 1 24.106 28.329 2.891 1.00 0.00 JH ATOM 10 CD CYC 1 24.941 26.784 4.162 1.00 0.00 JH ATOM 11 HD1 CYC 1 24.135 26.825 4.896 1.00 0.00 JH ATOM 12 HD2 CYC 1 25.727 27.444 4.533 1.00 0.00 JH ATOM 13 CE CYC 1 25.482 25.349 4.056 1.00 0.00 JH ATOM 14 HE1 CYC 1 24.665 24.668 3.814 1.00 0.00 JH ATOM 15 HE2 CYC 1 25.875 25.027 5.021 1.00 0.00 JH ATOM 16 CF CYC 1 26.577 25.242 2.982 1.00 0.00 JH ATOM 17 HF1 CYC 1 27.448 25.821 3.290 1.00 0.00 JH ATOM 18 HF2 CYC 1 26.911 24.208 2.892 1.00 0.00 JH TER JH ENDMDL JH Here is the hdb entry. Add it to ffoplsaa.hdb: JH CYC 6 JH 24 HA CA CB CF JH 24 HB CB CA CC JH 24 HC CC CB CD JH 24 HD CD CC CE JH 24 HE CE CD CF JH 24 HF CF CE CA JH Here is the rtp entry. Add it to ffoplsaa.rtp and run pdb2gmx. JH ; cyclohexane JH [ CYC ] JH [ atoms ] JH CA opls_136 -0.120 1 JH HA1 opls_140 0.060 1 JH HA2 opls_140 0.060 1 JH CB opls_136 -0.120 2 JH HB1 opls_140 0.060 2 JH HB2 opls_140 0.060 2 JH CC opls_136 -0.120 3 JH HC1 opls_140 0.060 3 JH HC2 opls_140 0.060 3 JH CD opls_136 -0.120 4 JH HD1 opls_140 0.060 4 JH HD2 opls_140 0.060 4 JH CE opls_136 -0.120 5 JH HE1 opls_140 0.060 5 JH HE2 opls_140 0.060 5 JH CF opls_136 -0.120 6 JH HF1 opls_140 0.060 6 JH HF2 opls_140 0.060 6 JH [ bonds ] JH CA HA1 JH CA HA2 JH CA CF JH CA CB JH CB HB1 JH CB HB2 JH CB CC JH CC HC1 JH CC HC2 JH CC CD JH CD HD1 JH CD HD2 JH CD CE JH CE HE1 JH CE HE2 JH CE CF JH CF HF1 JH CF HF2 JH Vitaly Chaban wrote: Guys, Does anybody have an already prepared topology of cyclohexane? Thanks. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ 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] RE: GROMACS sample procedure
I am new to GROMACS and have not tried any calculation using it. I have installed grmx on scientific linux. Can anyone help me find a sample procedure of using GROMACS for molecular dynamics simulation (or even for simple energy calculation)? I am interested in doing research on Molecular Dynamics using GROMACS, but so far, I really dont have an idea where to start. I hope to hear your advise. Thank you very much /usr/local/gromacs/share/gromacs/tutor/ -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ 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] RE: using vmd output for MDRUN
Following is the scenario I am trying for MDS I am using vmd to modify the position of my molecule, and then output from vmd is in .pdb format. for .top file I have generated those files from pdb2gmx and edited them manually as suggested in drug-enzyme tutorial by J E Kerrigan. Now, I am in doubt weather I can use the .pdb from vmd .top file for running editconf and genbox followed by MDS ? Why not? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ 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] GROMACS sample procedure
I think there are example files, look at the gromacs web site. A super brief answer would be as follows: File.top is the topology file. It holds description of atom types potentials. File.gro holds the initial coordinates, and box dimensions. File.mdp holds run parameters (how many steps, temperature, output control, simulation type, etc`). The command grompp reads some input files, and prepares file.tpr, which is then used as an input to mdrun - the ultimate command that does the actual MD. The number of different initials of G.R.O.M.A.C.S., minus the nearest prime number is 17. Gromacs has healing powers. Please refer to the gromacs manual for more details, and to the gromacs wiki aswell. Omer Markovitch. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Sep 18, 2008 at 12:03, Christopher Ambe [EMAIL PROTECTED]wrote: I am new to GROMACS and have not tried any calculation using it. I have installed grmx on scientific linux. Can anyone help me find a sample procedure of using GROMACS for molecular dynamics simulation (or even for simple energy calculation)? I am interested in doing research on Molecular Dynamics using GROMACS, but so far, I really dont have an idea where to start. I hope to hear your advise. Thank you very much Christopher Ambe MSU-Iligan Institute of Technology ___ 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 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] Re: still system exploid
Finally i succeed to run my simulation. I change the define section from DPOSRES to DFLEXIBLE and also I chnge the number of LINC iteration from 4 to 8. I also minimized the system by l-bfgs (as you said). Now the system is running and till now it don't have any problem. I don't now this change are good or not but still my system is running. I believe you can decrease LINCS iterations back to 4 when your system is properly equilibrated. Do you have any other suggestion for me? I think it is a good illustration that the problem in most such cases is particles overlaps in the initial configurations. So be further careful to avoid such situations. thank you very much. Morteza -Vitaly -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ 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] simulation in vacuum
@ David: Thanks for the paper. (Patriksson et al. Biochemistry 46 pp. 933-945 (2007)) But how can I turn the Cut-Offs off? Think it's best to describe first what I do: I simulate pulling experiments of a small model system (consisting of two ureas with short alkane linkers). In the future I want to simulate two fixed chains which are connected by pairs of the small system and look how the pairs open. (Simulations in solvent will follow, but to see how it work, I think it is easier to start in vacuum). |---X X---| | | |---X X---| | | |---X X---| The system will look like that above (X are the ureas groups, which form hydrogen bonds). But first I want to simulate only one pair. The only way to use (effective) no Cut-Off, would be that I use an very large Cut-Off so that the molecules are all the time in it. But I think (after reading the paper) there is another way to do this. Regarding the protonating state, I think the molecules are not protonated. Thanks for all the help. Thomas ___ 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] Re:GROMACS sample procedure
Hi, Its good to chose Gromacs for running MDSimulations. Gromacs procedure cocern many tutorials are available in the net just type gromacs tutorials in google moreover check the gmx-archives regularly for finding solutions corresponding queries. Good luck. I am new to GROMACS and have not tried any calculation using it. I have installed grmx on scientific linux. Can anyone help me find a sample procedure of using GROMACS for molecular dynamics simulation (or even for simple energy calculation)? I am interested in doing research on Molecular Dynamics using GROMACS, but so far, I really dont have an idea where to start. I hope to hear your advise. Thank you very much Christopher Ambe MSU-Iligan Institute of Technology ___ 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 -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080918/8fe3ceaf/attachment-0001.html -- ___ 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! End of gmx-users Digest, Vol 53, Issue 93 * ___ 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] simulation in vacuum
Thomas Schlesier wrote: @ David: Thanks for the paper. (Patriksson et al. Biochemistry 46 pp. 933-945 (2007)) But how can I turn the Cut-Offs off? Set them to zero. And also nstlist = 0. Think it's best to describe first what I do: I simulate pulling experiments of a small model system (consisting of two ureas with short alkane linkers). In the future I want to simulate two fixed chains which are connected by pairs of the small system and look how the pairs open. (Simulations in solvent will follow, but to see how it work, I think it is easier to start in vacuum). |---X X---| | | |---X X---| | | |---X X---| The system will look like that above (X are the ureas groups, which form hydrogen bonds). But first I want to simulate only one pair. The only way to use (effective) no Cut-Off, would be that I use an very large Cut-Off so that the molecules are all the time in it. But I think (after reading the paper) there is another way to do this. Regarding the protonating state, I think the molecules are not protonated. Thanks for all the help. Thomas ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 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] regarding :RMSIP calculation
dear groacs users I want to calculate r.m.s.i.p for exploring convergence of my system and motions of two different proteins,i divided my trajectory in two equal parts and did g_covar for getting eigenvectors and corresponding eigenvector trjectory as trr file for C-alpha atom of 10 eigenvectors.even i know how to calculate RMSIP by trr file in Matlab but it is more time taking process because my system is quite large (509 residues).I need a script or tools to calculate it. before writting this mail i searched in gmx- mailing list and i did not find any script for same. need your help! thanks in advance. sanjay upadhyay research scholar proein dynamics lab IIT bombay India ___ 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 sasa 3.2.1 vs 3.3.2
Hi users: Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I make the analysis with GROMACS 3.3.2 and GROMACS 3.2.1 . When I do the sasa analysis I observe differences in the sasa values between the two versions. The total sasa seems to be same in the two graphs but the hydrophobic and hydrophilic looks very different (see attached pictures). What could be the problem? Which version will be the best for analysis? Cheers, Anthony attachment: Untitled.png___ 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] reg: vectors
Dear users, while calculating the correlation functions of a vector (using g_rotacf), are the vectors are normalized ? If not how can we obtain the correlation function with normalized vectors using gromacs tools ? ___ 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] regarding :RMSIP calculation
Hi Sanjay, You searched maybe..., but not good enough. Anyway, suits me for knowing that it sometimes helps adding my name to the search query :p :p :p http://www.gromacs.org/pipermail/gmx-users/2006-July/023049.html Hope it helps, Tsjerk On Thu, Sep 18, 2008 at 1:29 PM, [EMAIL PROTECTED] wrote: dear groacs users I want to calculate r.m.s.i.p for exploring convergence of my system and motions of two different proteins,i divided my trajectory in two equal parts and did g_covar for getting eigenvectors and corresponding eigenvector trjectory as trr file for C-alpha atom of 10 eigenvectors.even i know how to calculate RMSIP by trr file in Matlab but it is more time taking process because my system is quite large (509 residues).I need a script or tools to calculate it. before writting this mail i searched in gmx- mailing list and i did not find any script for same. need your help! thanks in advance. sanjay upadhyay research scholar proein dynamics lab IIT bombay India ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem sasa 3.2.1 vs 3.3.2
Hi Anthony, It's not even that different. The order is swapped (the colors) and the most notable difference is that the noise is higher in the newer version. The running averages will probably give very similar results. Still interesting to know what happened to the noise. The answer is probably in the source (and may be in a head belonging to a developer). Cheers, Tsjerk On Thu, Sep 18, 2008 at 3:39 PM, Anthony Cruz [EMAIL PROTECTED] wrote: Hi users: Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I make the analysis with GROMACS 3.3.2 and GROMACS 3.2.1 . When I do the sasa analysis I observe differences in the sasa values between the two versions. The total sasa seems to be same in the two graphs but the hydrophobic and hydrophilic looks very different (see attached pictures). What could be the problem? Which version will be the best for analysis? Cheers, Anthony ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dna-protein complex simulation
Dear users, I am trying to run a simulation of SNA-protein complex. I have changed DA,DC,DT,DG to DADE,DCYT,DTHY,DGUA and all ' to *. while running the PDB2GMX command, I am getting following error *Program pdb2gmx, VERSION 3.3.2 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom P in residue THF 2 not found in rtp entry with 39 atoms while sorting atoms * but THF 2 atom is not present in my pdb file.How can I remove this error? Thanx in advance -- PRASUN (ASHOKA) ___ 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
