Re: [gmx-users] Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
Hi! Thanks for your helps! Fulya ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Need a vacation? Get great deals to amazing places on Yahoo! Travel. ___ 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] grompp error
Hello all, I am trying to minimise a structure having 3 chains and each of having 90 residues. While running grompp , I got following error. Please tell me how to fix this error. Thanking you in advance . creating statusfile for 1 node... checking input for internal consistency... calling /usr/bin/cpp... human_resistin_A43_mut_D43.top:11:23: error: ffG43a1.itp: No such file or directory human_resistin_A43_mut_D43.top:19:19: error: spc.itp: No such file or directory human_resistin_A43_mut_D43.top:29:20: error: ions.itp: No such file or directory cpp exit code: 256 Tried to execute: '/usr/bin/cpp -I:/home/soft/GromacSingle/share/gromacs/top:/home/soft/GromacSingle/share/gromacs/top -DFLEX_SPC human_resistin_A43_mut_D43.top grompp6I6a2P' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... Cleaning up temporary file grompp6I6a2P --- Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive moleculetype, file human_resistin_A43_mut_D43_A.itp, line 10 --- Confirmed (Star Trek) -- Dhananjay ___ 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] grompp error
Dhananjay wrote: Hello all, I am trying to minimise a structure having 3 chains and each of having 90 residues. While running grompp , I got following error. Please tell me how to fix this error. chapter 5. wiki.gromacs.org Thanking you in advance . creating statusfile for 1 node... checking input for internal consistency... calling /usr/bin/cpp... human_resistin_A43_mut_D43.top:11:23: error: ffG43a1.itp: No such file or directory human_resistin_A43_mut_D43.top:19:19: error: spc.itp: No such file or directory human_resistin_A43_mut_D43.top:29:20: error: ions.itp: No such file or directory cpp exit code: 256 Tried to execute: '/usr/bin/cpp -I:/home/soft/GromacSingle/share/gromacs/top:/home/soft/GromacSingle/share/gromacs/top -DFLEX_SPC human_resistin_A43_mut_D43.top grompp6I6a2P' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... Cleaning up temporary file grompp6I6a2P --- Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive moleculetype, file human_resistin_A43_mut_D43_A.itp, line 10 --- Confirmed (Star Trek) -- Dhananjay ___ 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. 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
Re: [gmx-users] grompp error
Dhananjay wrote: Hello all, I am trying to minimise a structure having 3 chains and each of having 90 residues. While running grompp , I got following error. Please tell me how to fix this error. Thanking you in advance . creating statusfile for 1 node... checking input for internal consistency... calling /usr/bin/cpp... human_resistin_A43_mut_D43.top:11:23: error: ffG43a1.itp: No such file or directory human_resistin_A43_mut_D43.top:19:19: error: spc.itp: No such file or directory human_resistin_A43_mut_D43.top:29:20: error: ions.itp: No such file or directory If cpp can't find these, you haven't sourced GMXRC properly. Mark ___ 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] Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
fulya caglar wrote: Hi! Thanks for your helps! Fulya So what was the problem, please? I'd like to make an entry in our FAQ list so others can solve this problem quicker. Mark ___ 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] Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
I have not solved my problem exactly,yet.But now it is more clear for me now and I just want to thank you for your help.As soon as possible I will finish my simulations and I let you know what the proplem was. Fulya Mark Abraham [EMAIL PROTECTED] wrote: fulya caglar wrote: Hi! Thanks for your helps! Fulya So what was the problem, please? I'd like to make an entry in our FAQ list so others can solve this problem quicker. Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online.___ 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] Alpha-Helix Dipole
Hi David, I tried to use the option -mutot in g_energy, but all I get is the component dipoles. They match what I've got in the file Mtot.xvg from g_dipoles, which is really high (for all the system: water+ polyala helix, fluctuates between 100 and 300 D), but in adip.xvg (the average) the value in each time is very low (around 2.3 D). The index file contains only the standard options (protein, SOL, backbone, etc..) and when I try to select backbone (e.g. in g_dipoles) it gives the fatal error: The index group is not a set of whole molecules. Why is the Mtot like this and what exactly does the average mean? Anyway, thanks for all the guidance, it helped a lot! I tried to make it objective now and this is the last question I send you, for not wasting your time! If I can't conclude anything, can you send me any reference, or some exercises which I could compare some results and see if what I'm doing is right or what to expect from the dipole calculation? (I think that the structures are ok for the QM, but just I wanted to confirm if that situation is the closest that we have for the helix in water) Thank you very much (sorry if any of the questions seemed stupid!) Gustavo [EMAIL PROTECTED] wrote: Just one more thing, David. I read the manual, but I couldn't realize: is the average dipole, (at the top of the g_dipoles output) the overall dipole of the system? (also in the adip.xvg, plotted against time). Because all I want to know is whether the system has a low dipole moment (which in the case of polyala+h2o, the average is 2.3 D) depends on your index file. the total dipole is also stored in the energy file, so you can run g_energy to get it out, or g_dipoles -enx to compute dielectric constants etc. Gustavo [EMAIL PROTECTED] wrote: Hi David Thank you very much for the reply! So, which group, in the end, shall I select in g_dipoles to see the dipole? And how to use trjconv after editconf the way you told me? (the input/output of editconf is a .gro file and of trjconv is .trr/.xtc files) And whose group shall I select in the least squares/output prompts in trjconv -fit trans+rot? Thank you very much, Gustavo I would do both the helix backbone, and the entire helix, so that you can test whether the sidechains compensate for the net dipole or the other way around. You could also look at the net dipole of the water with resect to the helix. As for trjconv, please read the manual about aligning structures (trjconv -h) Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. 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 This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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. 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 This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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
Re: [gmx-users] Correlation Matrix Calculation
Sorry for the confusion . I want the correlation. So I can just use g_covar to get the covar. matrix, and divide each term by what you stated, to get the correlation matrix? (if I follow you correctly). Thanks, Hi Arneh, You're not clear on what you want. Is it a covariance matrix or a correlation matrix. Correlation and covariance are different things. g_covar lets you write out a covariance matrix using the option -ascii. In case you want the correlation matrix (though IIRC Karplus also used the covariance matrix), you have to divide each element m_ij by sqrt(m_ii)*sqrt(m_jj). Cheers, Tsjerk On 8/31/07, Arneh Babakhani [EMAIL PROTECTED] wrote: Can anyone briefly recommend a procedure for calculating the correlation matrix (not the diagonalized covariance matrix, as done by g_covar) of a specified group? In particular, I'm looking to calculate the covariance matrix, as specifed in the Karplus paper (Proteins: Vol 11:205-217, 1991), where each entry of the matrix is defined as the correlation between the i-th and j-th atom: c_ij = delta r_i delta r_j where delta r is the deviation of i from its average position, averaged over the ensemble. Or, is there a way to use g_covar and suppress the diagonalization step, so as to obtain only the translation correlation matrix??? (I couldn't find anything to this effect in the manual). Much thanks, Arneh ___ 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] Correlation Matrix Calculation
Yes, I have seen this, had trouble compiling it. Does it matter what version of gromacs you're trying to compile it with? Hi, On Friday, 31. August 2007 05:14, Arneh Babakhani wrote: Can anyone briefly recommend a procedure for calculating the correlation matrix (not the diagonalized covariance matrix, as done by g_covar) of a specified group? In particular, I'm looking to calculate the covariance matrix, as specifed in the Karplus paper (Proteins: Vol 11:205-217, 1991), where each entry of the matrix is defined as the correlation between the i-th and j-th atom: c_ij = delta r_i delta r_j where delta r is the deviation of i from its average position, averaged over the ensemble. Or, is there a way to use g_covar and suppress the diagonalization step, so as to obtain only the translation correlation matrix??? (I couldn't find anything to this effect in the manual). take a look at Generalized Correlation for Biomolecular Dynamics from Lange and Grubmueller: http://www.mpibpc.gwdg.de/groups/grubmueller/start/people/olange/gencorr.html Much thanks, Arneh greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) â 9131 â 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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] what is the force function for proper dihedrals
Hi Chris, I've been searching for this as well. You might get some clues in the following article, but I didn't have time to read it: T. Schlick, A Recipe for Evaluating and Differentiating Cos phi Expressions, J. Comp. Chem., 10:951-956, May (1989) I'm interested if you find any pointer to a book or paper on this issue. Cheers, Patrick Chris Neale a écrit : Hello, The manual does a good job at explaining the potential energy function for all types of interactions. For bonded interactions the manual also describes the force function for every type except dihedrals. The Allan and Tildesley bool also lacks this information. It's one thing to know that the force is the negative gradient of the potential energy, but for proper dihedrals it is not trivial to determine this. If anybody knows the force function for proper dihedrals then I would greatly appreciate a reply. Thanks, Chris. ___ 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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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] Fullerene simulation
Dear all, Is anybody studied with fullerene MD simulation using gromacs before? (I searched in literature, unfortunately I couldn't find). Best Wishes, Serdar - Yahoo! Clever - Sie haben Fragen? Yahoo! Nutzer antworten Ihnen.___ 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] g_bundle usage
Hi The protein in my simulations has two distinct domains and some interdomain motion is seen on the simualtion timescale. I was wanting to define a helix in domain 1 and one in domain 2 and track their movement relative to each other. For this I was going to use g_bundle. I have tried this but I am doing something wrong as I get the error: Fatal error: The size of one of your index groups is not a multiple of n I have defined the groups in my index file: helix 1 helix 2 and after entering: g_bundle -s md1.tpr -f protein.xtc -n index.ndx -tu ns (I have also tried with -na 2) I use these groups as input to the program and then get the error. I think I may have misunderstood the documentation, can someone please suggest how to perform this analysis correctly?! Thanks Jo ___ 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] Measure contour area of bilayer undulation
Dear gmx-users, This is not a question about Gromacs, but I wonder if I can hear suggestions from here. I would like to measure contour area of bilayer undulation. If there is no undulation, area (area per lipid) can be easily calculated by dividing XY area by number of lipid. But, in the lipid bilayer with undulation, how can contour area (ultimately, area per lipid) be calculated ? If there are some suggestions about possibilities in Gromacs or other tools, it'd be really appreciated. Thanks, best, Hwankyu. ___ 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] Measure contour area of bilayer undulation
Hi, In principle you can calculate this from equations e.g. in Safran's book Statistical Thermodynamics of Surfaces, Interfaces, and Membranes. However, when we worked with this a few years ago we ended up in the conclusion that for the properties we were interested in, the effective area/lipid measured in experiments was better approximated by the cell dimensions including fluctuations. YMMV, though! Cheers, Erik On Aug 31, 2007, at 10:22 PM, Hwankyu Lee wrote: Dear gmx-users, This is not a question about Gromacs, but I wonder if I can hear suggestions from here. I would like to measure contour area of bilayer undulation. If there is no undulation, area (area per lipid) can be easily calculated by dividing XY area by number of lipid. But, in the lipid bilayer with undulation, how can contour area (ultimately, area per lipid) be calculated ? If there are some suggestions about possibilities in Gromacs or other tools, it'd be really appreciated. Thanks, best, Hwankyu. ___ 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] Fwd: what is the force function for proper dihedrals
Haven't looked into the details yet, but this is worth noting for those interested. Thanks William. - Forwarded message from [EMAIL PROTECTED] - Date: Sat, 01 Sep 2007 00:15:25 -0400 From: William Noid [EMAIL PROTECTED] Reply-To: William Noid [EMAIL PROTECTED] Subject: what is the force function for proper dihedrals To: [EMAIL PROTECTED] howdy, i am guessing that you want a formula for the cartesian force on the atoms involved in a 4-body bonded interaction that is parameterized by a dihedral angle. if so then all you have to do (of course) is to work out a sort of nasty jacobian transforming the coordinates, but of course it is kind of messy/cumbersome and easy to make a mistake. the only published place i know where they have the answer explicitly is in the dl_poly manual, which you can find at http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/. they work it out in gory detail on page 18 of the manual (which is actually page 30 of the pdf file). i can't promise there are no typos there, but i think it is quite likely correct. i have explicitly checked their calculation for valence angles, though this is considerably easier. but at least this would give you something to check against. one warning in advance: the dl_poly folks define vectors in the opposite convention from normal. see in the figure that r_ij is the vector from i to j - whereas i would have defined r_ij as the vector from j to i. anyway, i hope this is helpful. if this is what you wanted maybe you could forward the info to the mailing list. if not, sorry to cause you any bother. peace, will noid - End forwarded message - ___ 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
