[gmx-users] Nucleic acid simulation
Hello every one, Im interesting in performing a MD for Protein - RNA complex , Can any one suggest a good tutorial. Thanks in advance. -- Ravi Raja Tejasvi . Merugu http://www.rsquarelabs.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] bindng energy H bond energy calculation
Thanks Mr.Justin,, I will try them .. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] bindng energy H bond energy calculation
Dear all, Can any one help e regarding 1.) I want to find the binding energy of ligand with the protein , and 2.) Hydrogen Bond energy of the protein ligand interactions (for H-bond ).. and 3 ) if possible H bond distances along the time scale(say 10ns). Is there any way 4 ) to measure the contribution of hydrophobic / philic interactions of the protein active site with ligands binding energy.. 5) to calculate the distance between the residues(let say Tyr and Arg) in my protein. (Actually I want to check a key interaction between them) Thanks in advance. Ravi Raja Tejasvi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Water-Mediated Hydrogen Bonds
Dear All, I’m doing research in the field of Protein-DNA interaction. I have gone through these papers, *A “Solvated Rotamer” Approach to Modeling Water-Mediated Hydrogen Bonds at Protein–Protein Interfaces* *“Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study”* *“Molecular Dynamics Simulation Study of Interaction between Model Rough Hydrophobic Surfaces.”* *“Prediction of Protein Binding to DNA in the Presence of Water-Mediated Hydrogen Bonds”* I have found lot of interesting things on these papers that will be useful for the progress of my research carrier. I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond and water mediated free energy in Gromacs ? Is there any way to calculate water mediated hydrogen bond between Protein-DNA using Gromacs tools? If it is possible, please send your program (water mediated hydrogen bond derivation program) to me and also the program operating procedure. Eagerly waiting for your reply. Thanking You Faithfully Raja -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs to Amber trajectory
Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory file to Amber trajectory file format. So that I can easily analyses this trajectory. I tried to convert Gromacs trajectory file to Amber trajectory file using VMD. This VMD converted trajectory is not working fine. Pls help me in this regards Eagerly waiting for your suggestion. Regards Raja -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs to Amber trajectory
Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory file to Amber trajectory file format. So that I can easily analyses this trajectory. I tried to convert Gromacs (.xtc) trajectory file to Amber (.mdcrd) trajectory file using VMD. This VMD converted trajectory is not working fine for DCCM (Dynamic cross correlation Matrix) analysis. Now i'm trying to convert Gromacs trajectory into dcd format, and then use ptraj to read the dcd file and write the mdcrd (or AMBER netcdf) trajectory. Example: --- [1] Gromacs20ns.xtc à nojump.xtc (using trjcat/trjconv) [2] nojump.xtc à amber20ns.dcd (using VMD) [3] Ptraj file conversion trajin amber20ns.dcd trajout amber20ns.nc netcdf (or) Is it necessary to do image for this file. trajin test.dcd center origin image origin center trajout amber20ns.nc netcdf Is this correct procedure? I want to do DCCM (Dynamic cross correlation analysis). DCCM Ptraj file trajin test.rst7 trajin amber20ns.nc strip :WAT strip :Cl- center :1-85 origin image origin center matrix correl name corr @CA out amber20ns.dccm byres If you have any ptraj file format for this. Actually i did simulation based on NPT ensemble. Is it necessary to mention the BOX dimensions in any were in the dcd file creation? Already i tried to convert Gromacs trajectory into PDB (total trajectory) but it is not working well for the analysis purpose of AMBER. Eagerly waiting for your suggestion Regards Raja On Fri, Jun 17, 2011 at 6:46 AM, Mark Abraham mark.abra...@anu.edu.auwrote: ** On 17/06/2011 2:57 AM, Raja Pandian wrote: Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory file to Amber trajectory file format. So that I can easily analyses this trajectory. I tried to convert Gromacs trajectory file to Amber trajectory file using VMD. This VMD converted trajectory is not working fine. Pls help me in this regards You really haven't said what you've done at the critical point, nor why you think it is not working. So we are unable to help at this time. Maek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem in downloading source code
Dear Mark, Thanks for your reply. But still I am unable to download , and with same error reported in the downloading page as mentioned in my previous mail. Others membering from different locations reading this mail could please test the link and report here would be useful for me. The browser that I use for downloading, is Internet explorer of windowsXP. With thanks, B.Nataraj On Tue, 23 Oct 2007 16:21:44 +1000, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Dear sir, There is a problem in accessing your site for downloading gromacs source code files. The following errors shows in the page for ftp download. ISA Server: extended error message : 200 Switching to Binary mode. 200 PORT command successful. Consider using PASV. 425 Failed to establish connection. ### And I also tried the alternative option given in the website , web interface to ftp server. But that page also end up in showing Page not found error. Kindly get into the problem. Downloading 3.3.2 source works fine for me. 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 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ 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 in downloading source code
Hi Florian, Thanks for your reply. I tried to ftp through wget...but still not workingI pasted the output of wget hereunder. # D:\Biosoftwares\wgetwget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz --14:11:41-- ftp://ftp.gromacs.org:21/pub/gromacs/gromacs-3.3.2.tar.gz = `gromacs-3.3.2.tar.gz' Connecting to ftp.gromacs.org:21... connect: No such file or directory Retrying. --14:12:02-- ftp://ftp.gromacs.org:21/pub/gromacs/gromacs-3.3.2.tar.gz (try: 2) = `gromacs-3.3.2.tar.gz' Connecting to ftp.gromacs.org:21... connect: No such file or directory Retrying. --14:12:23-- ftp://ftp.gromacs.org:21/pub/gromacs/gromacs-3.3.2.tar.gz (try: 3) = `gromacs-3.3.2.tar.gz' Connecting to ftp.gromacs.org:21... # The try is going on and on Please suggest me any other alternative.. With thanks ! B.Nataraj On Tue, 23 Oct 2007 09:51:57 +0200, Florian Haberl [EMAIL PROTECTED] said: Hi, On Tuesday, 23. October 2007 09:24, raja wrote: Dear Mark, Thanks for your reply. But still I am unable to download , and with same error reported in the downloading page as mentioned in my previous mail. Others membering from different locations reading this mail could please test the link and report here would be useful for me. The browser that I use for downloading, is Internet explorer of windowsXP. try something like wget wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz --09:50:53-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz = `gromacs-3.3.2.tar.gz' Resolving ftp.gromacs.org... 130.238.41.205 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD /pub/gromacs ... done. == PASV ... done.== RETR gromacs-3.3.2.tar.gz ... done. Length: 8,019,795 (7.6M) (unauthoritative) works here fine. greetings, Florian With thanks, B.Nataraj On Tue, 23 Oct 2007 16:21:44 +1000, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Dear sir, There is a problem in accessing your site for downloading gromacs source code files. The following errors shows in the page for ftp download. ISA Server: extended error message : 200 Switching to Binary mode. 200 PORT command successful. Consider using PASV. 425 Failed to establish connection. ### And I also tried the alternative option given in the website , web interface to ftp server. But that page also end up in showing Page not found error. Kindly get into the problem. Downloading 3.3.2 source works fine for me. 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 -- raja [EMAIL PROTECTED] -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) #8722; 9131 #8722; 85 26573 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 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Choose from over 50 domains or use your own ___ 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] Source code through email
Dear listmembers, I am already running gromacs earlier version, now when I try to upgrade to newer version, I could not download latest source code from the gromacs website. If anyone have the latest gromacs release gromacs-3.3.2.tar.gz with them, please send it to me through email. With thanks, B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? ___ 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 in downloading source code
Dear sir, There is a problem in accessing your site for downloading gromacs source code files. The following errors shows in the page for ftp download. ISA Server: extended error message : 200 Switching to Binary mode. 200 PORT command successful. Consider using PASV. 425 Failed to establish connection. ### And I also tried the alternative option given in the website , web interface to ftp server. But that page also end up in showing Page not found error. Kindly get into the problem. Sincerely, B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ 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: Re: [gmx-users] Error while compilation of Gromacs3.3.1.....in SGI Octane
The indicated format string requires additional arguments. %s (%s)\n\n\n,BUILD_TIME,BUILD_USER,BUILD_MACHINE); ^ cc-1018 cc: ERROR File = main.c, Line = 247 An unmatched left parentheses ( appears in an expression. %s (%s)\n\n\n,BUILD_TIME,BUILD_USER,BUILD_MACHINE); ^ cc-1008 cc: ERROR File = main.c, Line = 247 A new-line character appears inside a string literal. %s (%s)\n\n\n,BUILD_TIME,BUILD_USER,BUILD_MACHINE); ^ 2 errors detected in the compilation of main.c. *** Error code 1 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) How can I correct this error?Where is the main.c ? Kindly tell me if I have to set some parameters while compilation. regards sharada___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - One of many happy users: http://www.fastmail.fm/docs/quotes.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] AMBER atom type for Hydroxamate moeity
Dear gmxions, I am writing a topology for a ligand using AMBER99 force field convention. The ligand contains the hydroxamate group, for your quick reference I have drawn it below O HO|| \ / \ N Please let me know which atoms type in amber can be used for these atoms Especially the Nitrogen atom in this group. Since I am using carbonyl group and hydroxyl group atoms types for oxygen (But I am not sure of its validity). Please help me to chose appropriate atoms type. I also pasted available atom types for Nitrogen in AMBER99 force field. amber99_3414.01000 ; N sp2 nitrogen in amide groups amber99_3514.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) amber99_3614.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) amber99_3714.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) amber99_3814.01000 ; N2 sp2 N in amino groups amber99_3914.01000 ; N3 sp3 N for charged amino groups (Lys, etc) amber99_4014.01000 ; N* sp2 N With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The professional email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] AMBER atom type for Hydroxamate moeity
Thanks Mark for your reply. And sorry about missing one hydrogen in my drawn topology... B.Nataraj On Thu, 30 Nov 2006 23:12:10 +1100, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Dear gmxions, I am writing a topology for a ligand using AMBER99 force field convention. The ligand contains the hydroxamate group, for your quick reference I have drawn it below O HO|| \ / \ N Your N has an unsatisfied valence... what's missing? (Don't bother to tell me, it doesn't matter) Please let me know which atoms type in amber can be used for these atoms Especially the Nitrogen atom in this group. Since I am using carbonyl group and hydroxyl group atoms types for oxygen (But I am not sure of its validity). Please help me to chose appropriate atoms type. Probably, none of them. Force fields are not magic numbers that can be applied to all possible types of atoms. They are constructs designed to be reliably applicable to fairly narrow sets of atom types under the range of conditions they were parametrized with (also normally narrow). You will see this when you read the paper that describes the development process of this force field. Notwithstanding, people routinely abuse them with gay abandon, probably on the bad advice of others, or their own experience of the fairly good transferability of quantum-chemical methods. Your only vaguely reliable course is to find a set of experimental data consistent with those used for the development of the force field, work out what new values you need to derive and to follow a process to optimize those values to reproduce the experimental data. This process is not for the inexperienced, or for the faint of heart. Otherwise, you'll have the usual expensive random number generator. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - mmm... Fastmail... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] AMBER atom type for Hydroxamate moeity
Hi Florian, Thanks for your mail and introducing me the Antechamber site. I am trying out there in that site. B.Nataraj On Thu, 30 Nov 2006 16:00:39 +0100, Florian Haberl [EMAIL PROTECTED] said: hi, On Thursday 30 November 2006 13:01, raja wrote: Dear gmxions, I am writing a topology for a ligand using AMBER99 force field convention. The ligand contains the hydroxamate group, for your quick reference I have drawn it below O HO|| \ / \ N Please let me know which atoms type in amber can be used for these atoms Especially the Nitrogen atom in this group. Since I am using carbonyl group and hydroxyl group atoms types for oxygen (But I am not sure of its validity). Please help me to chose appropriate atoms type. A more practical not theoretical idea: Use antechamber from Amber suite, it is a nice tool for parametrising unknown small molecules (http://amber.scripps.edu/antechamber/antechamber.html). In the Amber9 handbook (page 74 around) i is described how to use it and i think there is a tutorial on the AMBER site around. Fitting of charges will be calculated with gaussian or other ab initio suits. After preparing such a file you can load it in Leap (similar to pdb2gmx) and you can complete your input, top and coordinate file will be written, both can be transfered to gromacs inputs and after calculation you can use all gromacs tools for analysis. Of course check the in- and output of antechamber, especially atomtypes! I also pasted available atom types for Nitrogen in AMBER99 force field. amber99_3414.01000 ; N sp2 nitrogen in amide groups amber99_3514.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) amber99_3614.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) amber99_3714.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) amber99_3814.01000 ; N2 sp2 N in amino groups amber99_3914.01000 ; N3 sp3 N for charged amino groups (Lys, etc) amber99_4014.01000 ; N* sp2 N With thanks! B.Nataraj -- raja [EMAIL PROTECTED] Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) #8722; 9131 #8722; 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 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 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access all of your messages and folders wherever you are ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] AMBER atom type for Hydroxamate moeity
Hi nr, Thanks for your mail. Yea, I am looking for parameters like you mentioned than partial charges. B.Nataraj On Thu, 30 Nov 2006 09:40:03 -0800, Nathan C. Rockwell [EMAIL PROTECTED] said: Hydroxamates are also a bit tricky chemically; their chemistry is different than carboxylates or amides, so parameters for the ASP or ASN side chains are unlikely to work. There are also some really old papers from Gilchrist Jencks on alpha-effect nucleophiles that are good examples of why hydroxylamine can't be thought of as a simple amine. Therefore, I would suggest a complete parametrization (measuring things like the force constants for stretching the N-O bond, torsion about it, and so on) rather than just getting partial charges. It would seem likely to give better results. cheers, nr On 11/30/06 7:00 AM, Florian Haberl [EMAIL PROTECTED] wrote: hi, On Thursday 30 November 2006 13:01, raja wrote: Dear gmxions, I am writing a topology for a ligand using AMBER99 force field convention. The ligand contains the hydroxamate group, for your quick reference I have drawn it below O HO|| \ / \ N Please let me know which atoms type in amber can be used for these atoms Especially the Nitrogen atom in this group. Since I am using carbonyl group and hydroxyl group atoms types for oxygen (But I am not sure of its validity). Please help me to chose appropriate atoms type. A more practical not theoretical idea: Use antechamber from Amber suite, it is a nice tool for parametrising unknown small molecules (http://amber.scripps.edu/antechamber/antechamber.html). In the Amber9 handbook (page 74 around) i is described how to use it and i think there is a tutorial on the AMBER site around. Fitting of charges will be calculated with gaussian or other ab initio suits. After preparing such a file you can load it in Leap (similar to pdb2gmx) and you can complete your input, top and coordinate file will be written, both can be transfered to gromacs inputs and after calculation you can use all gromacs tools for analysis. Of course check the in- and output of antechamber, especially atomtypes! I also pasted available atom types for Nitrogen in AMBER99 force field. amber99_3414.01000 ; N sp2 nitrogen in amide groups amber99_3514.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) amber99_3614.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) amber99_3714.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) amber99_3814.01000 ; N2 sp2 N in amino groups amber99_3914.01000 ; N3 sp3 N for charged amino groups (Lys, etc) amber99_4014.01000 ; N* sp2 N With thanks! B.Nataraj -- raja [EMAIL PROTECTED] Greetings, Florian ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] AMBER atom type for Hydroxamate moeity
Hi Mark, Thanks again, But I am Indian...will either of those flavour work for me :-) B.Nataraj On Fri, 01 Dec 2006 16:21:59 +1100, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Hi Goette, Thanks for your mail. I have just find an article done a similar work...I am trying to reach them to get their parameters. Unfortunately I am not having Gaussian. Can you suggest me some other freely available quantum mechanics software ? GAMESS should get the job done. It comes in two flavours, US and UK. Google will find it :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - mmm... Fastmail... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Script for coverting ITP and gro file to Autodock pdbqs
Hi Mahnam, Thanks for your mail. Sorry, I do not get you whether you are talking on charge based on individual residue or on whole protein. As for as I know, autodock is not allowing non integer charge on residue basis and which implies that whole protein can also, should not have non integer as net formal charge and zero is not mandatory. Please reply me. B.Nataraj On Wed, 29 Nov 2006 19:16:52 +0330, Mahnam [EMAIL PROTECTED] said: In God We Trust Hello Dear raja I think that the charges in itp of Gromacs don't match with charges in Autodock.Becase the total charge in Autodock is zero ,but the total charges in itp of Gromacs are not zero ,then you can't use gromacs charge for Autodock. Sincerely yours Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tue, 28 Nov 2006 12:47:14 +1100 Subject: Re: [gmx-users] Script for coverting ITP and gro file to Autodock pdbqs raja wrote: Hi gmxions, I want to use charge information contained in itp file produced in gromacs for docking purpose (Autodock). Kindly share a script if anyone written to convert information content from gromacs protein's itp (for charge) and gro (coordinate) information to autodock pdbqs or pdbq formated one. This sounds like a good exercise for learning how to use Perl. Get the file format descriptions and read a few chapters of a Perl reference. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Partial charge distribution for metal ligating atoms
Dear Mark, Thanks for your reply. Well, I have well taken your point of making separate charge group constituting Zn and its residues and I am working out for it, in mean time I need some clarification in my present approach. I just detailed out my earlier mail hereunder. I am using AMBER force field. This is default partial charge distribution for deprotonated Cystine CYM N -0.4157 CYM H 0.2719 CYM CA -0.0351 CYM HA 0.0508 CYM CB -0.2413 CYMHB1 0.1122 CYMHB2 0.1122 CYM SG -0.8844 CYM C 0.5973 CYM O -0.5679 Formal Charge = -1.0 Now my modified partial charge at SG to -0.6944 CYM N -0.4157 CYM H 0.2719 CYM CA -0.0351 CYM HA 0.0508 CYM CB -0.2413 CYMHB1 0.1122 CYMHB2 0.1122 CYM SG -0.6944 CYM C 0.5973 CYM O -0.5679 Formal Charge = -0.8100 --- According to manual, to ensure integer value of total charge on the residue CYM (cysteine). Ideally, following the force field convention, I would like to do readjustment of the individual partial charges to make it as total = -1. But on other hand this is my intuition that, formal charge for -1 for CYM is applicable for free Cysteine residue in AMBER force field, but in my case, it is harmonically bonded with zinc and also the charge transfer is taken place. This makes me to think that the formal charge of CYM should be adjusted to neutral. Please give your thought? With thanks ! B.Nataraj On Tue, 28 Nov 2006 17:51:04 +1100, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Hi gmxions, There are many references, say that Zn2+ partial charge should be reduced to ~0.7 rather than the force field default value of 2. In line with that there are many values published for distributed charge in its surrounding ligand atoms in compensation for loss of positive charge of Zn. OK, so this strategy preserves charge neutrality over the zinc and a bunch of ligand residues. It will not preserve charge neutrality of the individual residues, obviously. Now I am having set of values to be distributed for my system's active site residues, say for one SG-Cys, and two NE2-His atoms. My question is that what will be net formal charge for these residues after its specific atoms' charges are modified. The old value, plus the modification? In other words, for example, after modifying default partial charge of SG-Cys from -0.8844 to -0.6944, Should I adjust its net formal charge to -1 or to 0? Not sure where you're adjusting the net formal charge or why you think it's necessary. What you really want to do is have charge groups with integral values of charge (see section 3.4.2 and some part of Chapter 5 for how to do this), so that probably means combining the zinc with chunks of these residues into one large +2 charge group. Then on what basis I can adjust rest of the atoms#8217; partial charges. Why would you do this? Whatever you do should be consistent with the most reliable scheme in the literature, unless you want to create an expensive random number generator. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Partial charge distribution for metal ligating atoms
Thanks Goette for your mail. So system neutrality is restored as per your advice but individual residue will deviate from its integer value (formal charge), wont violate anything? I remember once I read the lines of individual residues' partial charge should be an integer from gromacs manual, I really took some time to search it in manual to refer that line in this mail, but I could not find it. But I am also using Autodock (Docking tool), where the non-integral charge on residue based is not allowed. May be I overlapped these two programs concept of partial charges! By, B.Nataraj the desired partial charge On Tue, 28 Nov 2006 11:48:40 +0100, Maik Goette [EMAIL PROTECTED] said: Hi Depends on your system, but in principle yes. A Cystein should be neutral. If you take a deprotonated one to build a complex with the zinc, it should be neutral afterwards. Lets assume a case with HIS/HIS/CYS as complex partners. the resdiues without a complex are assumed to be neutral. Therefore, their charges added should be 0. Add your zinc to the complex, take a partial charge of 0.7xx for it and modify the charges of the complex partners (i.e. the S and in the case of histidine it makes sense to spread the charge difference over the ring). If you now add up all the charges of all complex partners, the system should again be at charge 0. I can't see the problems, sorry. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ raja wrote: Dear Mark, Thanks for your reply. Well, I have well taken your point of making separate charge group constituting Zn and its residues and I am working out for it, in mean time I need some clarification in my present approach. I just detailed out my earlier mail hereunder. I am using AMBER force field. This is default partial charge distribution for deprotonated Cystine CYM N -0.4157 CYM H 0.2719 CYM CA -0.0351 CYM HA 0.0508 CYM CB -0.2413 CYMHB1 0.1122 CYMHB2 0.1122 CYM SG -0.8844 CYM C 0.5973 CYM O -0.5679 Formal Charge = -1.0 Now my modified partial charge at SG to -0.6944 CYM N -0.4157 CYM H 0.2719 CYM CA -0.0351 CYM HA 0.0508 CYM CB -0.2413 CYMHB1 0.1122 CYMHB2 0.1122 CYM SG -0.6944 CYM C 0.5973 CYM O -0.5679 Formal Charge = -0.8100 --- According to manual, to ensure integer value of total charge on the residue CYM (cysteine). Ideally, following the force field convention, I would like to do readjustment of the individual partial charges to make it as total = -1. But on other hand this is my intuition that, formal charge for -1 for CYM is applicable for free Cysteine residue in AMBER force field, but in my case, it is harmonically bonded with zinc and also the charge transfer is taken place. This makes me to think that the formal charge of CYM should be adjusted to neutral. Please give your thought? With thanks ! B.Nataraj On Tue, 28 Nov 2006 17:51:04 +1100, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Hi gmxions, There are many references, say that Zn2+ partial charge should be reduced to ~0.7 rather than the force field default value of 2. In line with that there are many values published for distributed charge in its surrounding ligand atoms in compensation for loss of positive charge of Zn. OK, so this strategy preserves charge neutrality over the zinc and a bunch of ligand residues. It will not preserve charge neutrality of the individual residues, obviously. Now I am having set of values to be distributed for my system's active site residues, say for one SG-Cys, and two NE2-His atoms. My question is that what will be net formal charge for these residues after its specific atoms' charges are modified. The old value, plus the modification? In other words, for example, after modifying default partial charge of SG-Cys from -0.8844 to -0.6944, Should I adjust its net formal charge to -1 or to 0? Not sure where you're adjusting the net formal charge or why you think it's necessary. What you really want to do is have charge groups with integral values of charge (see section 3.4.2 and some part of Chapter 5 for how to do this), so
Re: [gmx-users] Partial charge distribution for metal ligating atoms
Thanks Mark for your valuable suggestions and dedicating your valuable time for me. On Wed, 29 Nov 2006 00:47:33 +1100, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Thanks Goette for your mail. So system neutrality is restored as per your advice but individual residue will deviate from its integer value (formal charge), won#8217;t violate anything? A residue is an artificial grouping construct. There's nothing magical about them. Like I said before, you want neutral charge groups for a well-formed simulation with cut-offs. They are the relevant artificial grouping construct. I remember once I read the lines of individual residues' partial charge should be an integer from gromacs manual, I really took some time to search it in manual to refer that line in this mail, but I could not find it. Try reading the section reference I gave you earlier. But I am also using Autodock (Docking tool), where the non-integral charge on residue based is not allowed. May be I overlapped these two programs concept of partial charges! So redefine what a residue means! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Same, same, but different ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Inner product for two proteins eignevector trajectory
Hi gmxions, I like compute matrix of inner products using the command g_anaeig between eigenvector trr file of two different protein. When I do it, it shows error of dimension mismatch between two trr file, the error is understandable by me since eigen vectors computed for these two proteins are of different residue length, How to overcome this issue? Kindly reply me. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access all of your messages and folders wherever you are ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Script for coverting ITP and gro file to Autodock pdbqs
Hi gmxions, I want to use charge information contained in itp file produced in gromacs for docking purpose (Autodock). Kindly share a script if anyone written to convert information content from gromacs protein's itp (for charge) and gro (coordinate) information to autodock pdbqs or pdbq formated one. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - mmm... Fastmail... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Partial charge distribution for metal ligating atoms
Hi gmxions, There are many references, say that Zn2+ partial charge should be reduced to ~0.7 rather than the force field default value of 2. In line with that there are many values published for distributed charge in its surrounding ligand atoms in compensation for loss of positive charge of Zn. Now I am having set of values to be distributed for my system's active site residues, say for one SG-Cys, and two NE2-His atoms. My question is that what will be net formal charge for these residues after its specific atoms' charges are modified. In other words, for example, after modifying default partial charge of SG-Cys from -0.8844 to -0.6944, Should I adjust its net formal charge to -1 or to 0? Then on what basis I can adjust rest of the atoms partial charges. Kindly reply me. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Does exactly what it says on the tin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
Hi, If you want to get it go here(if you are luck) http://www.gromacs.org/contributed_by_users/task,cat_view/gid,39/ If you want to make one go here http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ If you want to learn how to make then get here http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf If you want to know more on this... search here http://www.gromacs.org/external/search.html By, B.Nataraj On Wed, 22 Nov 2006 23:33:55 -0800 (PST), hadi behzadi [EMAIL PROTECTED] said: Hello, all My question is how can I generate topology file for propanol compound and generate a suitable topology in water solvent. thanks a lot Thank a lot foryour guidance. - Want to start your own business? Learn how on Yahoo! Small Business. -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - One of many happy users: http://www.fastmail.fm/docs/quotes.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Script for atom typing for AMBER convention
Dear gmxions, I am searching for a script to convert the existing PDB (protein) files atoms and residues types to AMBER typing convention. I knew a script of this sort should be somewhere around...but after a long search, I could not spot it out. Please help me to spot it. I am using AMBER99 force field downloaded from ffAMBER site. By Thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ElecStatic for two residues and mdrun rerun issues
Thanks Mark for your reply. So the parameters nstlist=0, unconstrained_start=yes, using energygrp_excl will help to speed up the mdrun rerun ? , That is what I can understand after reading about those parameters picked up by you from manual. Before your mail reached, I ran rerun without any of those parameters changed in original mdp file but removed Protein, SOL, NA etc., from energygrp instead I put two groups representing two amino acid residues,whose potentials to be computed. It took half an hour for mdrun rurun for trajectory of 2ns length. So I will satisfied by my this run, if you can confirm me the introduction or alteration of those parameters is meant for only speedup purpose and not for anything else B.Nataraj On Wed, 22 Nov 2006 08:57:57 +1100, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Hi gmxions, I am interested in calculating electrostatic potential between chosen residues (Two amino acid) versus function of simulation time. To do that I have created two groups for two residues in index file and want to do #8220;mdrun rerun#8221; further. This is where I struggle; I am looking for some help to understand what is the mandatory adjustment in parameters to be effected before doing mdrun rerun. I don't think there are any mandatory adjustments, except, as the manual notes, you probably want nstlist=0, unconstrained_start=yes and to use energygrp_excl. I found this through the highly difficult process of searching the GROMACS manual for the word rerun. Perhaps you should do this too. I saw some replies regarding this issue by saying, #8220;setting bonded and LJ parameter to zero#8221; and more. This sounds like garbage, or something someone else was doing in their particular rerun. This quote would be more useful to everyone if you provided a link to the page you found it on. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ElecStatic for two residues and mdrun rerun issues
Dear Mark, Thanks for your untiring efforts to reply back to all. Regards, B.Nataraj On Wed, 22 Nov 2006 16:41:40 +1100, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Thanks Mark for your reply. So the #8220;parameters nstlist=0#8221;, #8220;unconstrained_start=yes#8221;, using #8220;energygrp_excl#8221; will help to speed up the mdrun rerun ? , That is what I can understand after reading about those parameters picked up by you from manual. Before your mail reached, I ran rerun without any of those parameters changed in original mdp file but removed #8220;Protein, SOL, NA etc.,#8221; from #8220;energygrp#8221; instead I put two groups representing two amino acid residues,whose potentials to be computed. It took half an hour for #8220;mdrun #8211;rurun#8221; for trajectory of 2ns length. So I will satisfied by my this run, if you can confirm me the introduction or alteration of those parameters is meant for only speedup purpose and not for anything else This is where you should be using your judgement, not mine. Why didn't doing the aforementioned reading, after the searching manual for rerun, answer your questions? I don't know anything about this issue except what I've read there... If you have a specific question about a fact or interpretation, then go right ahead and ask, but unless you're paying for a support and consultancy contract, nobody's going to go out of their way to do any work for you. :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access all of your messages and folders wherever you are ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Including water in for restraining
Hi Chris, Thanks for your detailed message and it is very helpful. B.Nataraj On Wed, 15 Nov 2006 22:01:32 -0500, [EMAIL PROTECTED] said: you are correct that you must include the water as part of the same molecule (as you appear to have already done for Zn). I assume that protein_ion_A.itp contains only one [ moleculetypes ] section that has the protein and also the zinc. Take a look at how Zn has been included there. Repeat this procedure to include the water that you want to be bonded. Then modify your coordinate file accordingly. You can get water parameters from gromacs-3.3.1/share/gromacs/top/tip3p.itp (or sub the name of your favourite water model). Note that this is intended as my best idea about how to go about doing exactly what you have asked. I have no idea how this is going to affect things like a temperature group that contains a protein, a zinc, and a single water if you have multiple temperature coupling groups. Also I am not sure if settle is going to work properly. There is no warranty associated with this next portion, I have never tried it. I have included this just to be explicit about what I am suggesting. Lets say you use tip4p and oplsaa: under [ atoms ] add: 2901 opls_1131 SOL OW 1 0.0 2902 opls_1141 SOL HW1 1 0.52 2903 opls_1141 SOL HW2 1 0.52 2904 opls_1151 SOL MW 1 -1.04 under [ bonds ] add: #ifdef FLEXIBLE ; i j funct length force.c. 2901 2902 2901 0.09572 502416.0 0.09572502416.0 2901 2903 2901 0.09572 502416.0 0.09572502416.0 #endif under [ angles ] add: #ifdef FLEXIBLE ; i j k funct angle force.c. 2902 2901 2903 1 104.52 628.02 104.52 628.02 #else [ settles ] ; OWfunct dohdhh 2901 1 0.095720.15139 #endif Then also add: [ exclusions ] 2901 2902 2903 2904 2902 2901 2903 2904 2903 2901 2902 2904 2904 2901 2902 2903 [ dummies3 ] ; Dummy fromfunct a b 2904 2901 2902 2903 1 0.128012065 0.128012065 Then go back and add any bonds that you want between this water and the protein or zinc. It is unclear to me if the [ exclusions ] section is necessary or even advisable. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] water in protein itp file
Dear Mark, Thaks for your replies and I end this discussion with this. B.Nataraj On Wed, 15 Nov 2006 11:51:37 +1100, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Dear Mark, Well and thanks again, QM-MM is a good option, as you said for analyzing the energetic of water ligating process. But my case not concerning to that process, rather study a system consists of a macromolecule as a whole, where this water bound zinc is a part of it. If this is a case of QM-MM to be done for this process, then how it is encouraged for other protein residues, like His NE2, Asp OD, GLU OD, atoms making similar interaction with metal ion to use harmonic bond constraints. When it is true and possible for amino acid ligating atoms, why it is not for oxygen atoms from a water molecule. Sorry, I don't understand the second half of this post. I appreciate that English isn't your native language, but can you express it in different words, please? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The professional email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Retaining water in protein chain
Dear gmxions, I want to retain one of water molecule in main chain of protein while converting it into separate chains as it is usualy done after genion using pdb2gmx. How can I do it ? With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access all of your messages and folders wherever you are ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] water in protein itp file
Dear Mark, Thanks for your immediate reply and good solution. But until before yours this mail, I was thinking that inclusion of water and restraining them with metal ion is a very common happening in MD. Since in my short spell of molecular modeling and drug design experience, I have found almost 75% of the drug targets are metalo-enzyme and if you can still probe its active site, can invariably find water ligating with metal in most of the cases (Say 90%). This water bound form is present until an external ligand or drug replace and ligate with metal ion for enzyme inhibition process. I am really wondering a case, which I think quite common, is not able to depict easily in gromacs. I am so interested to extend this topic, how other gromacs users depict this scenario in their simulation Am I doing any thing stupid, I doubt myself? Regards and thanks! B.Nataraj On Tue, 14 Nov 2006 14:49:27 +1100, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Dear gmxions, I want to include one crystal water within protein itp, to further restrict it by harmonic bond with metal ion at the active site. In other words, one of the water molecules to be treated just likes another protein residue by pdb2gmx. How to do that? Nobody here owes you an answer. This is a fiddly thing to do, and you will need to work the details out yourself. I can well understand nobody really wanting to get involved. I expect you'd need to 1. Add that water to the .gro file by hand after using pdb2gmx, using a residue name distinct from any name other waters might use. 2. Extend the protein+metal [ molecule ] section of your .top by hand to add that water, using the information in spc.itp as a model for the stuff you're going to need to make water fit. Also add the harmonic bond in here. 3. Then use editconf and/or genbox to generate the rest of the solvent, and massage the [ molecules ] section of your .top to have the appropriate stuff. 4. Sacrifice a goat at the full moon. Oh, and read Chapter 5 of the manual *really* thoroughly. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] water in protein itp file
Dear Mark, Well and thanks again, QM-MM is a good option, as you said for analyzing the energetic of water ligating process. But my case not concerning to that process, rather study a system consists of a macromolecule as a whole, where this water bound zinc is a part of it. If this is a case of QM-MM to be done for this process, then how it is encouraged for other protein residues, like His NE2, Asp OD, GLU OD, atoms making similar interaction with metal ion to use harmonic bond constraints. When it is true and possible for amino acid ligating atoms, why it is not for oxygen atoms from a water molecule. With thanks! B.Nataraj On Tue, 14 Nov 2006 15:22:30 +1100, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Dear Mark, Thanks for your immediate reply and good solution. But until before yours this mail, I was thinking that inclusion of water and restraining them with metal ion is a very common happening in MD. Since in my short spell of molecular modeling and drug design experience, I have found almost 75% of the drug targets are metalo-enzyme and if you can still probe its active site, can invariably find water ligating with metal in most of the cases (Say 90%). This water bound form is present until an external ligand or drug replace and ligate with metal ion for enzyme inhibition process. I am really wondering a case, which I think quite common, is not able to depict easily in gromacs. I am so interested to extend this topic, how other gromacs users depict this scenario in their simulation Am I doing any thing stupid, I doubt myself? If you actually want accurate energetics, you should really be looking at QM-MM simulations, which are a whole different ballgame in complexity and cost. I understand GROMACS does interface with GAMESS for these kinds of simulations, but that's where my knowledge ends. You should definitely do some literature reading on QM-MM simulations and see what software people have actually been using successfully. Probably, you should use that, rather than trying to make GROMACS do the job. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Does exactly what it says on the tin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RESP fitting using MOPAC
Hi Ran, Thanks for your suggestion. B.Nataraj On Fri, 10 Nov 2006 09:16:29 +0100, Ran Friedman [EMAIL PROTECTED] said: Hi, The setting of partial charges is a delicate matter. How you do it depends on your ligand, the force-field you use and computational power available to you. If you're just simulating a single protein, than I would use an ab-initio of DFT potential rather than semi-empirical one such (which is what MOPAC gives you). In general, I would try to work as the force-field developers did in developing the charges - which means that RESP would be the method of choice for AMBER but not necessarily for different FFs. You have free software that you can use for such calculations such as GAMESS-US and NW-CHEM (though you need to obtain a licence to use them). Ran. raja wrote: Hi gmxions, I have found many article for calculating partial charges for a ligand using RESP (restricted electro static fitting) within active site using gaussian. But I do not have gaussion, So Is it done also by MOPAC? And if it is so kindly refer me the protocol to do that. With thanks! B.Nataraj -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Including water in for restraining
Hi Chris, Thanks for your effort to write me the detailed reply. In fact I tried to put harmonic restraint to one water molecule bound on Zn2+ within the active site of protein of my interest. The crystal structure reports four ligating atoms with Zn2+, in addition to H20; other three are from two NE2 atoms from HIS and one SD atom from CYS residues. I wanted to use bonded harmonic potential restraints for all those atoms so I edited original protein_ion_A.itp file, which contains information for protein and Zn alone. This is the addition at the end of [bonds] section of protein_ion_A.itp done by me --- 1747 2900 6 0.206 1673.6 2442 2900 6 0.248 1673.6 2505 2900 6 0.250 1673.6 2905 2900 6 0.251 1673.6 Where 1747 , 2442, 2505 are atom numbers of NE2 of 2 HIS and SD of Cys, 2900 is the Zn2+ but 2905 is the water-oxygen atom number which I referred from protein.gro file and usage of this, is causing me the error which I posted in my previous mail regarding this topic. I think the water is to be placed in the same file for this to work...but how to do that is not clear to me.. since no separate itp file is not created for water topology within the folder, so I can merge them with protein_A_ion.itp file by any of the scripts available as per some pervious postings (http://www.gromacs.org/pipermail/gmx-users/2005-October/017359.html ) Hope you can help me better now. Thanks in advance! B.Nataraj On Sat, 11 Nov 2006 01:17:43 -0500, [EMAIL PROTECTED] said: While I am using harmonic restraint for water and Zn, I am unable to do so since the chain A itp file does not contain water, It shows error as follow --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1108 Fatal error: [ file Protein_ion_A.itp, line 5847 ]: Atom index (2905) in bonds out of bounds (1-2900) --- How to restraint molecule which is present in out of this itp file ? Look at the end of your topol.top file. Does it contain any mention of water, ions, or zinc? If not, then it should contain lines like this (although the exact nature will depend on the water model): ; Include water topology #include tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif Then in your .mdp file include the line define = -DPOSRES_WATER to position restrain the water. For Zn it will look like this ; Include generic topology for ions #include ions.itp This won't work for position restraints. Therefore first look at ions.itp. Notice that there are multiple entries for each ion that correspond to the forcefield that you are using. For this example, let's say that you are using opls-aa: You would then remove 2 the lines: ; Include generic topology for ions #include ions.itp and add the following lines in their place: ; Taken from OPLS-AA from gromacs-3.3.1 [ moleculetype ] ; molname nrexcl ZN2+1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 ZN2+1 ZN2+ZN 1 265.37000 #ifdef POSRES_ZN ; Position restraint for ZN2+ [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif Then in your .mdp file include the line define = -DPOSRES_ZN to position restrain the zinc. To constrain both, do define = -DPOSRES_WATER -DPOSRES_ZN Further, whatever file you are using that contains the position restraints for your protein... remove any lines that reference water or zinc. If you need further help, please specify exactly what you have done so far, where you got your files, and what the files look like. Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Or how I learned to stop worrying and love email again ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RESP fitting using MOPAC
Hi gmxions, I have found many article for calculating partial charges for a ligand using RESP (restricted electro static fitting) within active site using gaussian. But I do not have gaussion, So Is it done also by MOPAC? And if it is so kindly refer me the protocol to do that. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access all of your messages and folders wherever you are ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Simulation single unit of a dimer
Dear David, Thanks for your reply and your suggestion is helping me. By, B.Nataraj On Mon, 06 Nov 2006 09:12:32 +0100, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Dear gmxions, The protein, which I am going to simulate, is a dimer, but my study through MD is not related of dimer interaction but its catalytic activity. So my question is can I simulate a unit of the dimer? Will that system be physically right to simulate? The individual unit of the dimer is performing the same catalytic activity but act individually. Your thought for this question would be very useful for me. With thanks! B.Nataraj It depends, the dimer may give stability that is necessary for catalysis. To be on the safe side use the dimer. It will also give you twice the statistics for your analysis. If you'd use the monomer a referee will ask you whether that is justified as well. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Does exactly what it says on the tin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Simulation single unit of a dimer
Dear gmxions, The protein, which I am going to simulate, is a dimer, but my study through MD is not related of dimer interaction but its catalytic activity. So my question is can I simulate a unit of the dimer? Will that system be physically right to simulate? The individual unit of the dimer is performing the same catalytic activity but act individually. Your thought for this question would be very useful for me. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - IMAP accessible web-mail ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Req for computer config for windows to run gromacs
Dear David, Thanks, but Linux is not possible because of other users not aware of that OS. Well, can you make details for some best hardware configuration. With thanks! B.Nataraj On Tue, 29 Aug 2006 08:41:20 +0200, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Dear all, We are proposing to buy 5 computers, PC machines going to be used for general purpose as well as for running gromacs. The OS would be windowsXP. It would be more useful if you can suggest me some good configuration for this purpose. We are also planning cluster those PC for gromacs. With thanks! B.Nataraj Run Linux on them. It will save you a lot of problems... Otherwise you're on your own. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The professional email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Req for computer config for windows to run gromacs
Dear all, We are proposing to buy 5 computers, PC machines going to be used for general purpose as well as for running gromacs. The OS would be windowsXP. It would be more useful if you can suggest me some good configuration for this purpose. We are also planning cluster those PC for gromacs. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to use deprotonated Cys
Hi all, I have protein with cys in active site, and I want to use deprotonated cys. In manual for pdb2gmx clearly says on option of choosing Cys protonated state possibility but why that option not appearing while running pdb2gmx , just like for Arg, His, Asp and Glu. I read quite a lot of mails regarding this issue most of them are in 2004 archives. Hope things are now changed and I can get some direct solution for this from any of you. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Same, same, but different ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to use deprotonated Cys
Dear David, Thanks again, yes Cys is having fourth ligand as water to complete the tetrahedral geometry. So for, I used distance restraints to hold all ligands intact with Zn at active site. All I want to do is trying to simulate the structure to see the overall dynamics of protein; the default Cys (protonated) in that case will affect the dynamics of protein in big deal? Since I am not going to simulate any QM at active site. So your feedback will help me to stick on the current setting and go ahead for further simulation without further thinking of protonated state of Cys. With thanks! B.Nataraj On Fri, 25 Aug 2006 06:24:58 +0200, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Dear david, Thanks for your reply. There are two forms exist for the protein of my interest and one is native form and other is with ligand bound in it. In later form of crystal structure, Cys is found to be as CSD [side chain as -C-S(2OH)] and physically attached to the Zn ion (as per pdb connection record) at the active site. In native form, the Cys is as such but not connected with Zn (in pdb no connection record is found). I use the native form for the simulation; here I want to use Cys, as deprotonated Cys since I believe is the right way to treat Cys which is electorstaticaly ligating Zn along with other two partners,( 2 His NE2 atoms). Now please tell me how to treat this Cys in opls force field. you will have to generate a specbond.dat entry for Cys-Zn linkage, and also a Cys residue entry in rtp/hdb with appropriate charges. For this you may need to do quantum calculations or check the literature. I assume the Zn has other ligands too, so these should be taken into account as well. With thanks! B.Nataraj On Thu, 24 Aug 2006 17:21:22 +0200, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Hi all, I have protein with #8220;cys#8221; in active site, and I want to use deprotonated #8220;cys#8221;. In manual for #8220;pdb2gmx #8220; clearly says on option of choosing Cys protonated state possibility but why that option not appearing while running #8220;pdb2gmx#8221; , just like for #8220;Arg#8221;, #8220;His#8221;, #8220;Asp#8221; and #8220;Glu#8221;. I read quite a lot of mails regarding this issue most of them are in #8220;2004 archives#8221;. Hope things are now changed and I can get some direct solution for this from any of you. With thanks! B.Nataraj There is no support for a charged Cys in OPLS or GROMOS ffs, but in GROMOS you can have deprotonated CYS (cys1) with zero charge. Is the CYS not bound to anything? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Or how I learned to stop worrying and love email again ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to use deprotonated Cys
Dear David, Thanks for your support as you are always. Regards, B.Nataraj On Fri, 25 Aug 2006 06:46:19 +0200, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Dear David, Thanks again, yes Cys is having fourth ligand as water to complete the tetrahedral geometry. So for, I used distance restraints to hold all ligands intact with Zn at active site. All I want to do is trying to simulate the structure to see the overall dynamics of protein; the default Cys (protonated) in that case will affect the dynamics of protein in big deal? Since I am not going to simulate any QM at active site. So your feedback will help me to stick on the current setting and go ahead for further simulation without further thinking of protonated state of Cys. you need to have a good description of the Zn site. We previously used distance restraints for that (J. Comp. Aid. Mol. Des. 17 pp. 551-565 (2003)), but it depends on the distance S-Zn (and other ligands). What is particularly important is the charge distribution. You can not leave the proton on if it shouldn't be there. With thanks! B.Nataraj On Fri, 25 Aug 2006 06:24:58 +0200, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Dear david, Thanks for your reply. There are two forms exist for the protein of my interest and one is native form and other is with ligand bound in it. In later form of crystal structure, Cys is found to be as CSD [side chain as -C-S(2OH)] and physically attached to the Zn ion (as per pdb connection record) at the active site. In native form, the Cys is as such but not connected with Zn (in pdb no connection record is found). I use the native form for the simulation; here I want to use Cys, as deprotonated Cys since I believe is the right way to treat Cys which is electorstaticaly ligating Zn along with other two partners,( 2 His NE2 atoms). Now please tell me how to treat this Cys in opls force field. you will have to generate a specbond.dat entry for Cys-Zn linkage, and also a Cys residue entry in rtp/hdb with appropriate charges. For this you may need to do quantum calculations or check the literature. I assume the Zn has other ligands too, so these should be taken into account as well. With thanks! B.Nataraj On Thu, 24 Aug 2006 17:21:22 +0200, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Hi all, I have protein with #8220;cys#8221; in active site, and I want to use deprotonated #8220;cys#8221;. In manual for #8220;pdb2gmx #8220; clearly says on option of choosing Cys protonated state possibility but why that option not appearing while running #8220;pdb2gmx#8221; , just like for #8220;Arg#8221;, #8220;His#8221;, #8220;Asp#8221; and #8220;Glu#8221;. I read quite a lot of mails regarding this issue most of them are in #8220;2004 archives#8221;. Hope things are now changed and I can get some direct solution for this from any of you. With thanks! B.Nataraj There is no support for a charged Cys in OPLS or GROMOS ffs, but in GROMOS you can have deprotonated CYS (cys1) with zero charge. Is the CYS not bound to anything? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3
[gmx-users] Ploting xvg file in R statistic package
Hi all, Anyone know , to convert xvg formated data of gromacs for analysis in R statistical package. with thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_hbond account dieletric medium ?
Hi XAvier, Thanks again, I meant the resistance caused due to dielectric of water separating two charged residues. I doubt whether it will allow the transfer of charge between them in order for hydrogen bond to be effected. With regards, B.Nataraj On Thu, 03 Aug 2006 09:25:07 +0200, X.Periole [EMAIL PROTECTED] said: I have shown hydrogen bond formation between guanidino side chain of Arginine and carboxylate in sidechain of Aspartate out my simulation result using g_hbond. Now I see those two residues are well exposed in solvent. Since g_hbond compute hydrogen bonds based on only distance and angles, how I can prove that hydrogen bonds formed between those groups are by overcoming the dielectric medium of waters? What do you mean exactly by overcoming the dielectric medium of water ? XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_hbond account dieletric medium ?
Thanks spoel, The g_hbond merely report formation of hydrogen bonds because of two electronegative atoms come closure to certain distance and angle. The force field used to simulate is also not capable of modeling hydrogen bond (Afraid whether I am right). If the h_bond computes the hydrogen bonds inside the active site there is certainty is there since dielectric is low inside but in outside will it be right to compute the hydrogen bonds mere based on distance and angle between the two electronegative atoms present in bulk solvent. There could be mere electrostatic interaction. But how we can prove that proton is shared between those atoms. Sorry if I am making any mistake at fundamental level. With thanks! B.Nataraj On Thu, 03 Aug 2006 16:12:41 +0200, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Hi XAvier, Thanks again, I meant the resistance caused due to dielectric of water separating two charged residues. I doubt whether it will allow the transfer of charge between them in order for hydrogen bond to be effected. It's still unclear. The hydrogen bonds you find are there because they are apparently stronger than hbonds with water. However they will still be broken intermittently. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_hbond account dieletric medium ?
Dear Spoel,
Thank for your elaborate answer and references. Some times this forum
serves more than just for gromacs, yes it helps to understand some
basics understanding of physical chemistry. I learned lot of fundamental
concepts of protein modeling in this forum, which I could never
understand by reading a book or journal.
Regards,
B.Nataraj
in
On Thu, 03 Aug 2006 17:29:19 +0200, David van der Spoel
[EMAIL PROTECTED] said:
raja wrote:
Thanks spoel,
The g_hbond merely report formation of hydrogen bonds because of two
electronegative atoms come closure to certain distance and angle. The
force field used to simulate is also not capable of modeling hydrogen
bond (Afraid whether I am right). If the h_bond computes the hydrogen
bonds inside the active site there is certainty is there since
dielectric is low inside but in outside will it be right to compute the
hydrogen bonds mere based on distance and angle between the two
electronegative atoms present in bulk solvent. There could be mere
electrostatic interaction. But how we can prove that proton is shared
between those atoms.
Sorry if I am making any mistake at fundamental level.
OK, I see what you mean now. First whether or not there is a HBond is a
matter of taste. One can use a geometric criterion or an energy
criterion to decide that. In molecular modeling the transfer of a proton
is not taken into account explicitly. Sharing a proton does not exist in
reality, in my opinion, however one can have fast shuffling of a proton
between two sites, e.g. in the active site of HIV protease, where there
are two Asp residues, one of which is protonated.
The following references may be helpful:
@Article{Starr2000a,
author = {F. W. Starr and J. K. Nielsen and H. Eugene Stanley},
title ={Hydrogen-bond dynamics for the extended simple point
charge mo
del of water},
journal = {Phys. Rev. E},
year = 2000,
volume = 62,
pages ={579-587}
}
@Article{Spoel2006b,
author = {D. van der Spoel and P. J. van Maaren and P. Larsson
and N. Ti
mneanu},
title ={Thermodynamics of hydrogen bonding in hydrophilic and
hydrophobic media},
journal = {J. Phys. Chem. B},
year = 2006,
volume = 110,
pages ={4393-4398}
}
@Article{Modig2003a,
author = {K. Modig and B. G. Pfrommer and B. Halle},
title ={Temperature-dependent hydrogen bond geometry in
liquid water},
journal = {Phys. Rev. Lett.},
year = 2003,
volume = 90,
pages =075502
}
--
David.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se
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[gmx-users] g_hbond account dieletric medium ?
Hi all, I have shown hydrogen bond formation between guanidino side chain of Arginine and carboxylate in sidechain of Aspartate out my simulation result using g_hbond. Now I see those two residues are well exposed in solvent. Since g_hbond compute hydrogen bonds based on only distance and angles, how I can prove that hydrogen bonds formed between those groups are by overcoming the dielectric medium of waters? With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fe(II) at active site
Hi all, During the simulation of protein with Fe (II) ligating with 2 His and 1 Asp residues at active site, I set every thing right including Kb value but failed to deprotonate NE2 atoms of 2 His residues ligating that Fe(II). After 2ns simulation run, the average pdb structure shows that the flip of His ring out from Fe (II), but the Asp-oxygen moved much closer to Fe (II) than its original position. If I compute RMSF for Fe (II), showing value of 0 through out the simulation run. The RMSF 0 indicates Fe (II) originally retained in its position, but the ligating His flipped and Asp as a single residue held the Fe (II) at its original position. So now please tell me whether this simulation is valid? More all-globular validation of the entire simulation is perfect. Kindly give me yours valid opinion. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fe(II) at active site
Hi XAvier, Thanks for your opinion. This is my maiden attempt to simulate a protein so the reason for the mistake. If possible could you please refer me some paper, which describe the simulation of a system, contains Fe (II) at its active site. I tried my best, but could not find a one. By, B.Nataraj On Sat, 29 Jul 2006 13:34:37 +0200, X.Periole [EMAIL PROTECTED] said: During the simulation of protein with Fe (II) ligating with 2 His and 1 Asp residues at active site, I set every thing right including Kb value but failed to deprotonate NE2 atoms of 2 His residues ligating that Fe(II). What do you mean by failed ? This should not be a problem. You can choose the protonation state of a his ... check the ffXXX.rtp file. After 2ns simulation run, the average pdb structure shows that the flip of His ring out from Fe (II), but the Asp-oxygen moved much closer to Fe (II) than its original position. If I compute RMSF for Fe (II), showing value of 0 through out the simulation run. The RMSF 0 indicates Fe (II) originally retained in its position, 0 fluctuations at all !!! You fixed its position or something ? That does not seems right !! but the ligating His flipped and Asp as a single residue held the Fe (II) at its original position. So now please tell me whether this simulation is valid? The simulation that you discribe does not seem to be a good representation of your system ... XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Or how I learned to stop worrying and love email again ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?
Dear all, I have written small perl script to compute R.M.S.I.P.(Root mean square internal product) for comparing two eigen vectors set from two different simulation. I compared first 10 eigen vectors of each set. The strange thing is that while I compare eigen vectors of same simulation, it is showing a value of 0.54, but literature says, r.m.s.i.p of 1 indicates that the sets are identical, while a value of 0 indicates that the eigenvectors are orthogonal. I also confirmed my script validity by manually computing the R.M.I.P for small set of values. Could any body explain me a bit regarding this issue? With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?
Hi Tsjerk, Thanks for your reply. I used identical values of 10 eignevectors in two different file to compute r.m.s.i.p. I have pasted the link of the article from where I used the formula for r.m.s.i.p. More for some other cases of non-identical values, it slightly exceeds the value of 1 (e.g., 1.0352), Which I am thinking due to some numerical problem. But I am confident that my script exactly following what the formula indicated in the article as pasted hereunder. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1304087 With thanks ! B.Nataraj On Fri, 28 Jul 2006 11:32:04 +0200, Tsjerk Wassenaar [EMAIL PROTECTED] said: Hi Raja, Did you use the same eigenvectors from the same simulation over the same stretch of time? For two (parts of a) simulation(s) of the same system, the RMSIP value will only converge to one in the limit of infinite time, or on long time scales at least. The eigenvectors obtained from two different (parts of) simulations can vary if different parts of the conformational space are sampled or simply if the sampling is different, which will be almost always for a limited stretch of time. Best regards, Tsjerk On 7/28/06, raja [EMAIL PROTECTED] wrote: Dear all, I have written small perl script to compute R.M.S.I.P.(Root mean square internal product) for comparing two eigen vectors set from two different simulation. I compared first 10 eigen vectors of each set. The strange thing is that while I compare eigen vectors of same simulation, it is showing a value of 0.54, but literature says, r.m.s.i.p of 1 indicates that the sets are identical, while a value of 0 indicates that the eigenvectors are orthogonal. I also confirmed my script validity by manually computing the R.M.I.P for small set of values. Could any body explain me a bit regarding this issue? With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Does exactly what it says on the tin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?
Hi Tsjerk,
Here is the script I am using. I already checked the value computed by
this script with manually computed value for small set of 3 eigen
vectors in each file. As you already know the formula, so please check
it up by yourself. More I am not a regular programmer so this script is
written for some quick solution, so please do not expect perfection in
usage of commands.
#---Perl script for computing R.M.S.I.P.
value--
# each file eig1.xvg and eig2.xvg contain 10 eigenvectors
$F1 = eig1.xvg;
$F2 = eig2.xvg;
open(F1) or die(Could not open file.);
$N1 = 0;
foreach $line(F1)
{
$A = $line;
open(F2) or die(Could not open file);
foreach $line(F2)
{
$B = $line;
$N = ($A*$B)*($A*$B);
print $N \n;
$N1 = $N1 + $N ;
#print $N1 \n ;
}
close(F2)
}
print The Value of N1 is $N1 \n;
$N1 = $N1/10;
$N1 = sqrt ($N1);
print $N1;
close(F1) ;
#---End of
code---
With thanks !
B.Nataraj
On Fri, 28 Jul 2006 13:05:23 +0200, Tsjerk Wassenaar
[EMAIL PROTECTED] said:
Hi Raja,
I really don't get it. From the definition it follows directly that if
you have the same sets of eigenvectors, the RMSIP will be 1. Each
eigenvector from a set gives an inproduct of 1 with itself and of 0
with any of the others, yielding a total of 10 for the double sum...
etc. If you use the same set twice, you probably have a bug in your
script.
Besides, from the definition it also follows that the RMSIP can not
exceed 1. I think 3.5% error is quite a bit.
Tsjerk
On 7/28/06, raja [EMAIL PROTECTED] wrote:
Hi Tsjerk,
Thanks for your reply. I used identical values of 10 eignevectors in two
different file to compute r.m.s.i.p. I have pasted the link of the
article from where I used the formula for r.m.s.i.p. More for some other
cases of non-identical values, it slightly exceeds the value of 1 (e.g.,
1.0352), Which I am thinking due to some numerical problem. But I am
confident that my script exactly following what the formula indicated in
the article as pasted hereunder.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1304087
With thanks !
B.Nataraj
On Fri, 28 Jul 2006 11:32:04 +0200, Tsjerk Wassenaar
[EMAIL PROTECTED] said:
Hi Raja,
Did you use the same eigenvectors from the same simulation over the
same stretch of time? For two (parts of a) simulation(s) of the same
system, the RMSIP value will only converge to one in the limit of
infinite time, or on long time scales at least. The eigenvectors
obtained from two different (parts of) simulations can vary if
different parts of the conformational space are sampled or simply if
the sampling is different, which will be almost always for a limited
stretch of time.
Best regards,
Tsjerk
On 7/28/06, raja [EMAIL PROTECTED] wrote:
Dear all,
I have written small perl script to compute R.M.S.I.P.(Root mean square
internal product) for comparing two eigen vectors set from two different
simulation. I compared first 10 eigen vectors of each set. The strange
thing is that while I compare eigen vectors of same simulation, it is
showing a value of 0.54, but literature says, r.m.s.i.p of 1 indicates
that the sets are identical, while a value of 0 indicates that the
eigenvectors are orthogonal. I also confirmed my script validity by
manually computing the R.M.I.P for small set of values.
Could any body explain me a bit regarding this issue?
With thanks!
B.Nataraj
--
raja
[EMAIL PROTECTED]
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Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
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Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?
Hi Tsjerk,
Oops, I am sorry and thanks for your help and providing me the program.
With thanks!
B.Nataraj
On Fri, 28 Jul 2006 13:35:48 +0200, Tsjerk Wassenaar
[EMAIL PROTECTED] said:
Hi Raja,
Okay, you're not using the eigenvectors, you're using the
eigenvalues... The eigenvectors are written to a .trr or .xpm file, as
NxN matrices.
You can try the attached script (which I got from Isabella Daidone) on
the .xpm file.
Good luck,
Tsjerk
On 7/28/06, raja [EMAIL PROTECTED] wrote:
Hi Tsjerk,
Here is the script I am using. I already checked the value computed by
this script with manually computed value for small set of 3 eigen
vectors in each file. As you already know the formula, so please check
it up by yourself. More I am not a regular programmer so this script is
written for some quick solution, so please do not expect perfection in
usage of commands.
#---Perl script for computing R.M.S.I.P.
value--
# each file eig1.xvg and eig2.xvg contain 10 eigenvectors
$F1 = eig1.xvg;
$F2 = eig2.xvg;
open(F1) or die(Could not open file.);
$N1 = 0;
foreach $line(F1)
{
$A = $line;
open(F2) or die(Could not open file);
foreach $line(F2)
{
$B = $line;
$N = ($A*$B)*($A*$B);
print $N \n;
$N1 = $N1 + $N ;
#print $N1 \n ;
}
close(F2)
}
print The Value of N1 is $N1 \n;
$N1 = $N1/10;
$N1 = sqrt ($N1);
print $N1;
close(F1) ;
#---End of
code---
With thanks !
B.Nataraj
On Fri, 28 Jul 2006 13:05:23 +0200, Tsjerk Wassenaar
[EMAIL PROTECTED] said:
Hi Raja,
I really don't get it. From the definition it follows directly that if
you have the same sets of eigenvectors, the RMSIP will be 1. Each
eigenvector from a set gives an inproduct of 1 with itself and of 0
with any of the others, yielding a total of 10 for the double sum...
etc. If you use the same set twice, you probably have a bug in your
script.
Besides, from the definition it also follows that the RMSIP can not
exceed 1. I think 3.5% error is quite a bit.
Tsjerk
On 7/28/06, raja [EMAIL PROTECTED] wrote:
Hi Tsjerk,
Thanks for your reply. I used identical values of 10 eignevectors in two
different file to compute r.m.s.i.p. I have pasted the link of the
article from where I used the formula for r.m.s.i.p. More for some other
cases of non-identical values, it slightly exceeds the value of 1 (e.g.,
1.0352), Which I am thinking due to some numerical problem. But I am
confident that my script exactly following what the formula indicated in
the article as pasted hereunder.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1304087
With thanks !
B.Nataraj
On Fri, 28 Jul 2006 11:32:04 +0200, Tsjerk Wassenaar
[EMAIL PROTECTED] said:
Hi Raja,
Did you use the same eigenvectors from the same simulation over the
same stretch of time? For two (parts of a) simulation(s) of the same
system, the RMSIP value will only converge to one in the limit of
infinite time, or on long time scales at least. The eigenvectors
obtained from two different (parts of) simulations can vary if
different parts of the conformational space are sampled or simply if
the sampling is different, which will be almost always for a limited
stretch of time.
Best regards,
Tsjerk
On 7/28/06, raja [EMAIL PROTECTED] wrote:
Dear all,
I have written small perl script to compute R.M.S.I.P.(Root mean
square
internal product) for comparing two eigen vectors set from two
different
simulation. I compared first 10 eigen vectors of each set. The
strange
thing is that while I compare eigen vectors of same simulation, it
is
showing a value of 0.54, but literature says, r.m.s.i.p of 1
indicates
that the sets are identical, while a value of 0 indicates that the
eigenvectors are orthogonal. I also confirmed my script validity by
manually computing the R.M.I.P for small set of values.
Could any body explain me a bit regarding this issue?
With thanks!
B.Nataraj
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[gmx-users] R.M.S.I.P. calcuation Reg..
Hi all, How to calculate the r.m.s.i.p.(Root mean square inner product) value (or matrix) between set of many eigen vectors file. Is it possible in groamcs in-build utilities ? Thanks in advance ! By, B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - And now for something completely different ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ZN HIS binding
Hi, Try to use nonbonded harmonic potential term (bond type 6) with Kb value of 1673.6 KJ/mol nm2. I tried this value and it worked good for my simulation , please try a trail run and see for whether it restraints the crystallographic distances ,if yes can use it for your simulation. Regards, B.Natarj On Mon, 17 Jul 2006 16:21:42 -0300, Antonio Sergio Kimus Braz [EMAIL PROTECTED] said: Hi for all ... Can somebody help me, how to make a bonded interaction between HIS an Zinc atom ? I work with a metalloprotease and in this protein 3 HIS redisidues make bond with a Zn atom by its NE2 atoms I try form this bounds by pdb2gmx with option -his a show only this : Type a number:1 Which HISTIDINE type do you want for residue 141 0. H on ND1 only (HISA) 1. H on NE2 only (HISB) 2. H on ND1 and NE2 (HISH) 3. Coupled to Heme (HIS1) I need make more one option like Couple to Zinc (HISZ) I try it : i insert a line : in specbond.dat in top folder HIS NE2 1 ZIH ZN 1 0.25HISZZIH *in **6* CYS SG 1 CYS SG 1 0.2 CYS2CYS2 CYS SG 1 HEMEFE 2 0.25CYS2HEME CYS SG 1 HEMECAB 1 0.2 CYS2HEME CYS SG 1 HEMECAC 1 0.2 CYS2HEME HIS NE2 1 HEMEFE 1 0.2 HIS1HEME*HIS NE2 1 ZIH ZN 1 0.25HISZZIH* but it dont resolve my problem Thanks ! -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Hbond dynamic representation in MD movie
Hi all, Is there a tool known for displaying hbonds dynamically during gromacs trajectory visualization process and should also have facility to make MD movie out of it. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Analysing using InsighII Decipher
Dear All, Any strategy available for analyzing gromacs trajectory in insightII, Decipher module. Kindly let me know. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Choose from over 50 domains or use your own ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] analysing ndx file of g_hbond
Dear all, The index file produced by g_hbond listing many rows of hbonds making atoms combination. Is there a way to get the corresponding residue and atom name for those numbers by any of the gromacs program or if anyone having the script to do that, kindly pass it on to me. My primary objective is to know how many hbond listed in index file are belong to main chain atoms. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Shutting down in Windows2000
Dear Gmxions, While I run MD (Gromacs 3.3.1) in cygwin under windows2000 for 2ns, it shuts off automaticaly after 2days . It happened in two different machine installed windows2000 professional. Any previous experience by any of this sort ? But it works perfect for windowsXP. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Accessible with your email software or over the web ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Shutting down in Windows2000
Thanks Mark for your reply, I run MD for 100 (2ns) at dt = 0.002. In both occasion, shutdown happened during mid night at around 7800 steps. I could not fix the problem by looking at log file as it does not contain any information regarding this. Is it possible that the gromacs could influence the shutting down the system because of it struck at some level during the computation? One more additional information I would like to add here, I usually prepare all necessary files prior to full MD simulation in my system (windowsXP) and transform it to some other machine (windows2000) only for final production phase of MD run. Can it be the cause? With thanks! B.Nataraj On Mon, 12 Jun 2006 16:24:14 +1000, Mark Abraham [EMAIL PROTECTED] said: raja wrote: Dear Gmxions, While I run MD (Gromacs 3.3.1) in cygwin under windows2000 for 2ns, it shuts off automaticaly after 2days . It happened in two different machine installed windows2000 professional. Any previous experience by any of this sort ? Not that I've heard of... are we talking 48 hours +/- 5 minutes or are we talking anything between 30 and 60 hours? How many steps run? How big are the output files? But it works perfect for windowsXP. So maybe the problem is with Windows 2000, not gromacs. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - mmm... Fastmail... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Value for bonded force constant (Kb)
Hi Gmxions, The value Kb = 1673.6 KJ/mol nm2 working good for restraining distance (type6, Harmonic potential) between Fe(II) and corresponding ligating atoms N and O (of amino acids) at the end of 5000 steps of energy minimization. That is newly introduced Kb value is able to restraint at around 2-3 A (Which is the average value found from crystal structure) when comparing to more than 5A in the absence of Kb value. I am going to start MD with a hope that this success will also be there at the end of 2ns simulation Is there any second thought? With thanks! B.Nataraj On Wed, 10 May 2006 05:16:26 -0700, raja [EMAIL PROTECTED] said: Hi Mr Tsjerkw, Thanks for your mail. Infact I intented to attach the reference link but I missed it. Anyway here is the link where I taken the value of Kb. Infact the reference only talk between Fe and O atoms. I belive this value will be more reasonably for my purpose. I will update the outcome of the result of MD using this restraints after my work completes. In mean time here is the reference link http://www.jbc.org/cgi/content/full/280/51/42188 For quick find out on the page , use this key work force constant of 4.0 kcal/mol/Å2 and please let me know the validity of my judgement. With Thanks ! B.Nataraj On Wed, 10 May 2006 13:50:17 +0200, Tsjerk Wassenaar [EMAIL PROTECTED] said: Hi Raja, No objections from my side. But if you could also include the references resulting from your literature study, that would be nice to have in the archive (may save somebody searching the literature to find some iron - ligand parameters). Cheers, Tsjerk On 5/10/06, raja [EMAIL PROTECTED] wrote: Hi gmxions, Based on the litterature search , I am going to use Kb value of 4 Kcal/mol A2 (1673.6 KJ/mol nm2)as harmonic bonded force field constant(type 6) for restraining distance of Fe(II) ligated with atoms of 2 Nitrogen and 1 Oxygen. If any one having objection please correct me ): . With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - And now for something completely different ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Value for bonded force constant (Kb)
Hi gmxions, Based on the litterature search , I am going to use Kb value of 4 Kcal/mol A2 (1673.6 KJ/mol nm2)as harmonic bonded force field constant(type 6) for restraining distance of Fe(II) ligated with atoms of 2 Nitrogen and 1 Oxygen. If any one having objection please correct me ): . With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Value for bonded force constant (Kb)
Hi Mr Tsjerkw, Thanks for your mail. Infact I intented to attach the reference link but I missed it. Anyway here is the link where I taken the value of Kb. Infact the reference only talk between Fe and O atoms. I belive this value will be more reasonably for my purpose. I will update the outcome of the result of MD using this restraints after my work completes. In mean time here is the reference link http://www.jbc.org/cgi/content/full/280/51/42188 For quick find out on the page , use this key work force constant of 4.0 kcal/mol/Å2 and please let me know the validity of my judgement. With Thanks ! B.Nataraj On Wed, 10 May 2006 13:50:17 +0200, Tsjerk Wassenaar [EMAIL PROTECTED] said: Hi Raja, No objections from my side. But if you could also include the references resulting from your literature study, that would be nice to have in the archive (may save somebody searching the literature to find some iron - ligand parameters). Cheers, Tsjerk On 5/10/06, raja [EMAIL PROTECTED] wrote: Hi gmxions, Based on the litterature search , I am going to use Kb value of 4 Kcal/mol A2 (1673.6 KJ/mol nm2)as harmonic bonded force field constant(type 6) for restraining distance of Fe(II) ligated with atoms of 2 Nitrogen and 1 Oxygen. If any one having objection please correct me ): . With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Value for bonded force constant (Kb)
Dear gmxions, Could any one give me the value for bonded force constant (Kb) to be used for restraining ,F(II) and ligating atoms of proteins ( 2 HISs and 1 ASP)using harmonic potential (type 6). With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Insight for my EM output analysis
Hi all, Energy minimization of two proteins, two are same protein but differing in form in which it is available in PDB (ligand bound and bare active site). There are no different in secondary structure extension between these two proteins according to experimental structure. When I minimize these two proteins using Gromacs minimization engine, a part of the secondary structure in protein with bound ligand is lost (here secondary structure is referring a Helix), coincidently that is the region of interest for my study. That is, the mutant variant at that position having a role in substrate conversion effect. I repeated the protocol of minimization with more rigorous using more stringent parameter set but there is no effect. This is really adding more interest to my work. I feel that I got result even before the most rigorous part of real MD itself. Is it really some thing to be existed about? And is it something that Gromacs engine had found out, the imperfection in crystallographic solved structure. Kindly share similar experience, one had in this list, would be so interesting to hear and feel good about my on going work. With regards, B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to make the missing atom by PRODRG
Hi GMXIONS, A hydrogen atom attached to carboxylate oxygen is missing in output gro file for a ligand produced by DUNDEE PRODRG server. How to add that hydrogen manually , Is there way to do that in any of available software ? With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS Error in Gromacs-3.3.1 in pr simulation
796304720527360. 0.1090 2581 2582 84.10.1229 570227104415744. 0.1229 2581 2583 87.50.1335 1196486083739648. 0.1335 2583 2584 84.70.1449 1327802024460288. 0.1449 2583 2592 89.60.1449 12586908467068928. 0.1449 2584 2585 82.40.1090 373719230840832. 0.1090 2584 2586 84.70.1529 557193858383872. 0.1529 2584 2595 78.70.1522 384292635017216. 0.1522 2586 2587 87.80.1090 892299856838656. 0.1090 2586 2588 87.90.1090 784728240160768. 0.1090 2586 2589 89.80.1529 15541680610476032. 0.1529 2589 2590 89.80.1090 15088365065994240. 0.1090 2589 2591 89.80.1090 9667539739082752. 0.1090 2589 2592 89.90.1529 10028344909234176. 0.1529 2592 2593 89.90.1090 1246239862272. 0.1090 2592 2594 89.80.1090 11725056707133440. 0.1090 2595 2596 72.40.1229 89924292313088. 0.1229 2595 2597 72.20.1335 91336472526848. 0.1335 2597 2598 57.80.1010 10061090914304. 0.1010 2597 2599 98.20.1449 39730460753920. 0.1449 2599 2600 110.90.1090 46532917198848. 0.1090 2599 2601 106.00.1529 46532917198848. 0.1529 2601 2602 44.20.1090 0.1553 0.1090 2601 2603 39.50.1090 0.1453 0.1090 2601 2604 34.30.1529 0.1898 0.1529 2620 2623 103.50.1335 66480221716480. 0.1335 2621 2622 128.30.1080 65873083629568. 0.1080 2621 2625 107.40.1381 65873083629568. 0.1381 3752 3754 32.50.1335 0.1694 0.1335 3754 3755 36.30.1010 0.1322 0.1010 3754 3756 108.60.1449 4735754567680. 0.1449 3756 3757 109.40.1090 4735754567680. 0.1090 3756 3758 108.90.1529 4735754567680. 0.1529 3756 3762 108.10.1522 21307202732032. 0.1522 3758 3759 44.90.1090 0.1587 0.1090 3758 3760 48.40.1090 0.1669 0.1090 3758 3761 47.50.1090 0.1642 0.1090 3762 3763 107.50.1229 21170350981120. 0.1229 3762 3764 101.00.1335 77805429719040. 0.1335 3764 3765 97.30.1010 69634032140288. 0.1010 3764 3766 91.40.1449 639036104376320. 0.1449 3766 3767 91.80.1090 566860454035456. 0.1090 3766 3768 90.30.1529 2673548959154176. 0.1529 3766 3772 91.90.1522 623377257594880. 0.1522 3768 3769 90.00.1090 44817124740300800. 0.1090 3768 3770 90.10.1090 2501536055820288. 0.1090 3768 3771 90.10.1090 2454604411305984. 0.1090 3772 3773 101.00.1229 87566044889088. 0.1229 3772 3774 106.50.1335 86224681304064. 0.1335 3774 3775 110.70.1449 22357045411840. 0.1449 3774 3783 110.90.1449 22305962983424. 0.1449 3775 3776 110.90.1090 6515677200384. 0.1090 3775 3777 104.60.1529 6515677200384. 0.1529 3775 3786 114.20.1522 6515677200384. 0.1522 3777 3778 45.60.1090 0.1622 0.1090 3777 3779 46.50.1090 0.1638 0.1090 3780 3781 38.80.1090 0.1429 0.1090 3780 3782 36.60.1090 0.1391 0.1090 3780 3783 105.80.1529 6577432559616. 0.1529 3783 3784 111.00.1090 6577432559616. 0.1090 3783 3785 116.50.1090 6577432559616. 0.1090 3786 3787 35.90.1229 0.1680 0.1229 3786 3788 37.50.1335 0.1851 0.1335 Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) Help me to fix this problem ! With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access your email from home and the web ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Doubt in Distance Restraints
Hi Mr.Tsjerk, Thanks for your reply and I checked manual based on your suggestion. I just want to make it sure, Is it what the manual says while adding type 6 bond that is to edit the protein.top file under [bond] section so as to depict harmonic interaction between metal and ligating atoms. ### [ bonds ] ; aiaj functc0c1c2 c3 4734 37242 4734 28392 4734 28722 # Where 4734 is Fe(II) atom and 3724,2839,2872 are respective metal chelating atoms of protein. Is it ok ? With thanks ! B.Nataraj On Thu, 20 Apr 2006 10:11:34 +0200, Tsjerk Wassenaar [EMAIL PROTECTED] said: Hi Raja, You may be better off just adding bonds. I believe there was a bond type (type 6) which was especially useful (intended?) for keeping metals bound to a protein. Cheers, Tsjerk On 4/20/06, raja [EMAIL PROTECTED] wrote: Dear all, My intention is to restrict Fe(II) in active site by distance restraint protocol. Fe(II) is ligated by three amino acides' polar atoms respectively by (1) NE2 of HIS ,(2) NE2 of HIS (3) OD1 of ASP. The following is the disres itp file I used (copied from manual3.3). where I edited the atom number of aminoacids(3724,2839,2872) and Fe(II) as 4734. # disres.itp # [ distance restraints ] ; ai ajtypeindextype' low up1 up2 fac 3724 4734 1010.0 2.09 0.4 1.0 2839 4734 1010.0 2.25 0.4 1.0 2872 4734 1010.0 2.18 0.4 1.0 I do not understand the meaning of up2 and fac so I left with 0.4 and 1.0 as such as found in manual. In mdp file I added the following the commands ## full.mdp ## define = -DDISRES disre= Simple ### I expected these modifictions will restrict but those distances are not restraintedwhy ? Kindly explain me that wheather I need to change any other parameter . With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - IMAP accessible web-mail ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reg LAM version to use
Dear Mr.Yang Ye, I asked this question since I want to save some time, and use those time for my real research in gromacs. I already installed the latest version of LAM in cygwin. I am having problem in lambooting , which I am trying to resolve using LAM user list. In that juncture I dont want to have version incompatiability with gromacs3.3.1 when everything get smooth with LAM. You see, I am dedicating more time for these installation and configuring issues rather than really doing any research in my MD. Please give me proper answer. With regards , B.Nataraj On Sat, 15 Apr 2006 14:09:10 +0800, Yang Ye [EMAIL PROTECTED] said: raja wrote: Hi All, In GROMACS website, it is explicitly stated that LAM-7.0.6-5 as the version for MPI option. Should I stick on the version of lam stated in gromacs webpage or can I use the latest version of LAM-7.1.2. Will it make any difference for MPI enabled gromacs-3.3.1 ? With thanks! B.Nataraj try and you know. Yang Ye ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reg LAM version to use
Dear Mr.Yang Ye, Thanks for your reply and suggestion. I am really felt sorry for hurting you. I am aware of your hard work and continuous patronage of all users through this mailing list. Experts like you being there is absolutely necessary for peoples like me to master in this tool. Once again I put forward my real problem. As I want to run MD for the protein of many variant types (mutant models) , It is absolutely needed a high performance , I do have SGI machine but I am unable to compile in it. Regarding which I posted a week back in mailing list (http://www.gromacs.org/pipermail/gmx-users/2006-April/020969.html) still this is unanswered. So now I am planning for MPI option in windows (Cygwin). I request you that if you cannot provide solution for my compilation problem in SGI, kindly provide me the executables of GROMACS3.3.1 or GROMACS3.3 for SGI IRIX6.5. With thanks! B.Nataraj On Sat, 15 Apr 2006 15:28:51 +0800, Yang Ye [EMAIL PROTECTED] said: raja wrote: Dear Mr.Yang Ye, I asked this question since I want to save some time, and use those time for my real research in gromacs. I already installed the latest version of LAM in cygwin. I am having problem in lambooting , which I am trying to resolve using LAM user list. In that juncture I dont want to have version incompatiability with gromacs3.3.1 when everything get smooth with LAM. You see, I am dedicating more time for these installation and configuring issues rather than really doing any research in my MD. Please give me proper answer. Hi, Raja If you would like to mention about time, sorry to say that your mail is wasting many people's time on this list. We are just offering our advices with the limit of our experience. If the mail is about something we did before, we are kind to answer it. If the mail is about some thing we never tried, we may spend time in paying our time and resources in looking it up. This is how many mailing list works. The mailing list relies on everyone's input from his experience. If you go ahead to try LAM on cygwin with GROMACS, you are most welcomed to contribute your experience here. Also, research work is not only about getting the result. System building is also part of the training. The different proportion of Introduction, Methodology, Results in a paper is a good indicator for the work you shall allocate. To con't from my last mail, I would like to add this: GROMACS is not sensitive to LAM version while LAM on cygwin is another story. Yang Ye With regards , B.Nataraj On Sat, 15 Apr 2006 14:09:10 +0800, Yang Ye [EMAIL PROTECTED] said: raja wrote: Hi All, In GROMACS website, it is explicitly stated that LAM-7.0.6-5 as the version for MPI option. Should I stick on the version of lam stated in gromacs webpage or can I use the latest version of LAM-7.1.2. Will it make any difference for MPI enabled gromacs-3.3.1 ? With thanks! B.Nataraj try and you know. Yang Ye ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Does exactly what it says on the tin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs3.3.1 compilation error in SGI
Dear Mr. Erick and Mr. spoel, Sorry , I am not a programmer, so please let me know which file under the folder src I have to incorporate this change you are suggested. With thanks ! B.Nataraj On Fri, 07 Apr 2006 10:47:43 +0200, David van der Spoel [EMAIL PROTECTED] said: Erik Lindahl wrote: Hi Raja, Try changing the void on line 150 to char. gcc doesn't complain about this casting even with full warnings, so we missed one instance. Maybe you'd rather need pc = (void *)(pc + 8) or even better pc = (pc[8]) Erik On Apr 7, 2006, at 10:36 AM, raja wrote: Dear all, I just tried to install groamcs3.3.1, with a hope to overcome the earlier bug I posted for 3.3 version (http://www.gromacs.org/pipermail/gmx-users/2006-April/020850.html) .But an other error occured in groamcs3.3.1 in SGI compilation.. Error ### -I../../src -I../../include -DGMXLIBDIR=\/usr/local/gromacs/share/top\ -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c -o qm_gaussian.lo qm_gaussian.c cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/gromacs/share/top\ -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c qm_gaussian.c -Wp,-MDupdate,.deps/qm_gaussian.TPlo -o qm_gaussian.o source='gmx_fft_fftw3.c' object='gmx_fft_fftw3.lo' libtool=yes \ DEPDIR=.deps depmode=sgi /bin/sh ../../config/depcomp \ /bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/gromacs/share/top\ -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c -o gmx_fft_fftw3.lo gmx_fft_fftw3.c cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/gromacs/share/top\ -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c gmx_fft_fftw3.c -Wp,-MDupdate,.deps/gmx_fft_fftw3.TPlo -o gmx_fft_fftw3.o cc-3316 cc: ERROR File = gmx_fft_fftw3.c, Line = 186 The expression must be a pointer to a complete object type. pc += 8; ^ cc-3316 cc: ERROR File = gmx_fft_fftw3.c, Line = 190 The expression must be a pointer to a complete object type. pc += 8; ^ 2 errors detected in the compilation of gmx_fft_fftw3.c. *** Error code 1 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) # I am desparate to compile in SGI , Please help me. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] --http://www.fastmail.fm - Access all of your messages and folders wherever you are ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http
Re: [gmx-users] gromacs3.3.1 compilation error in SGI
Dear Mr.Lindahl,
But I have not edited that file gmx_chi.c for any reason. Only thing I
edited was the file gmx_fft_fftw3.c
for my previous error reported. The same version compiled fine in Cygwin
. But I need it in SGI for performace reason.
Please help me to compile it in SGI!
With regards,
B.Nataraj
On Fri, 7 Apr 2006 15:51:54 +0200, Erik Lindahl [EMAIL PROTECTED]
said:
Hi,
As far as I can see that file is perfectly valid ANSI C - there is no
executable statement in the declaration section.
Cheers,
Erik
On Apr 7, 2006, at 2:15 PM, raja wrote:
Hi users,
This is another error occured while compiling in SGI
##
#
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1086
A declaration cannot appear after an executable statement in a
block.
intndih,nactdih,nf;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1087
A declaration cannot appear after an executable statement in a
block.
real **dih,*trans_frac,*aver_angle,*time;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1088
A declaration cannot appear after an executable statement in a
block.
inti,j,**chi_lookup,*xity;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1090
A declaration cannot appear after an executable statement in a
block.
t_filenm fnm[] = {
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1106
A declaration cannot appear after an executable statement in a
block.
int npargs;
^
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1107
A declaration cannot appear after an executable statement in a
block.
t_pargs *ppa;
^
20 errors detected in the compilation of gmx_chi.c.
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
You have new mail
##
##
Please help me !
With thanks !
B.Nataraj
On Fri, 7 Apr 2006 13:15:12 +0200, Erik Lindahl [EMAIL PROTECTED]
said:
Hi Raja,
Don't remove the asterisk - that is what makes it a pointer. The
declaration should be
char * pc;
Cheers,
Erik
On Apr 7, 2006, at 12:43 PM, raja wrote:
Dear Mr.Lindhal and Mr.Goel,
Based on your previous mail , I did these modification in
gmx_fft_fftw3.c
##
int
gmx_fft_init_1d_real(gmx_fft_t * pfft,
int nx)
{
gmx_fft_t fft;
real*p1,*p2,*up1,*up2;
char pc;
pc = (pc[8]);
int i,j,k;
if(pfft==NULL)
{
##
##
But I got these errors...
### ERROR
##
cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include
-DGMXLIBDIR=\/usr/local
/gromacs/share/top\ -I/usr/local/include -r12000 -mips4 -O3
-OPT:IEEE_arithmeti
c=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1
-LNO:ou_further=3 -O
PT:Olimit=0:roundoff=3:alias=typed -woff 1174 -
D__INLINE_INTRINSICS -c
gmx_fft_f
ftw3.c -Wp,-MDupdate,.deps/gmx_fft_fftw3.TPlo -o gmx_fft_fftw3.o
cc-1138 cc: ERROR File = gmx_fft_fftw3.c, Line = 151
Expression must have pointer-to-object type.
pc = (pc[8]);
^
cc-1551 cc: WARNING File = gmx_fft_fftw3.c, Line = 151
The variable pc is used before its value is set.
pc = (pc[8]);
^
cc-1241 cc: ERROR File = gmx_fft_fftw3.c, Line = 152
A declaration cannot appear after an executable statement in a
block.
int i,j,k;
^
cc-1515 cc: ERROR File = gmx_fft_fftw3.c, Line = 186
A value of type void * cannot be assigned to an entity of type
char.
pc = (void *)p1;
^
cc-1515 cc: ERROR File = gmx_fft_fftw3.c, Line = 190
A value of type void * cannot be assigned to an entity of type
char.
pc = (void *)p2;
^
4 errors detected in the compilation of gmx_fft_fftw3.c.
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
##
###
Did I do any thing wrong in modification ?
Thanks !
B.Nataraj
On Fri, 7 Apr 2006 11:37:21 +0200, Erik Lindahl
[EMAIL PROTECTED]
said:
Hi,
It says in the error message - here's the full path:
gromacs-3.3.1/src/mdlib/gmx_fft_fftw3.c.
Cheers,
Erik
On Apr 7, 2006, at 11:15 AM, raja wrote:
Dear Mr. Erick and Mr. spoel,
Sorry , I am not a programmer, so
Re: [gmx-users] configure problem in SGI
Dear Mr.Spoel, Thanks for your reply. Yea I checked , the corresponding files are there is /usr/local/lib. Totally 8 files and 1 folder called pkgconfig. More I also tried to set envirnomental variable to CPPFLAGS and LDFLAGS as command before configure but no effect. May I have to add these environmental variables in my .cshrc file ?. Please suggest me any other flags to be enabled or disabled to make configure to get path of fftw library files. With thanks! B.Nataraj On Mon, 03 Apr 2006 09:06:22 +0200, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Dear gmxions, I tried to compile gromacs in SGI IRIX6.5. I followed configuring and installing of fftw, both single and double precision as per gromacs website. When I tried to configure gromacs...it says.. Cannot find any single precision fftw.h or sfftw.h. I also checked the /usr/local/include/. The folder contains 2 files fftw3.f and fftw3.h. More I had the experince of compiling under cygwin. So I did crosscheck for files under folder in cygwin (/usr/local/include/ ) found exactly same files there too as fftw3.f and fftw3.h. But the configuration of gromacs worked in cygwin without any error, otherhand why it fails in SGI ? Please help me out ! Maybe you explicitly have to add /usr/local/include to the CPPFLAGS environment variable. Do you have the corresponding libraries in /usr/local/lib? I also pasted detailed error output while configuring gromacs in SGI. ### checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... no checking dynamic linker characteristics... irix6.5 ld.so checking whether ln -s works... yes checking for sqrt in -lm... yes checking for fftw.h... no checking for sfftw.h... no configure: error: Cannot find any single precision fftw.h or sfftw.h Do you have single precision FFTW installed? If you are using packages, note that you also need fftw-devel to compile GROMACS. You can find the software at www.fftw.org, and detailed instructions at www.gromacs.org. If you compiled FFTW yourself: Note that the default FFTW setup is double precision. Change the FFTW configuration to single with --enable-float. If you want MPI support, use --enable-mpi. It is a good idea to install both single double. If your sysadm doesn't want to install it you can do it to a location in your home directory and provide the correct paths in .. ### With thanks ! B.Nataraj -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] configure problem in SGI
Dear Mr Erik, No, I use fftw-3.0.1 and gromacs-3.0.1 and more I have not selected FFTW-2 manually. With thnaks B.Nataraj On Mon, 3 Apr 2006 10:05:53 +0200, Erik Lindahl [EMAIL PROTECTED] said: Hi, Please read through and follow the detailed installation instructions at http://www.gromacs.org/installation/index.php Based in the limited output below it looks as if you are either trying to install an earlier version of Gromacs without support for FFTW-3, or you have manually selected FFTW-2. Cheers, Erik On Apr 3, 2006, at 9:44 AM, raja wrote: Dear Mr.Spoel, Thanks for your reply. Yea I checked , the corresponding files are there is /usr/local/lib. Totally 8 files and 1 folder called pkgconfig. More I also tried to set envirnomental variable to CPPFLAGS and LDFLAGS as command before configure but no effect. May I have to add these environmental variables in my .cshrc file ?. Please suggest me any other flags to be enabled or disabled to make configure to get path of fftw library files. With thanks! B.Nataraj On Mon, 03 Apr 2006 09:06:22 +0200, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Dear gmxions, I tried to compile gromacs in SGI IRIX6.5. I followed configuring and installing of fftw, both single and double precision as per gromacs website. When I tried to configure gromacs...it says.. Cannot find any single precision fftw.h or sfftw.h. I also checked the /usr/local/include/. The folder contains 2 files fftw3.f and fftw3.h. More I had the experince of compiling under cygwin. So I did crosscheck for files under folder in cygwin (/usr/local/include/ ) found exactly same files there too as fftw3.f and fftw3.h. But the configuration of gromacs worked in cygwin without any error, otherhand why it fails in SGI ? Please help me out ! Maybe you explicitly have to add /usr/local/include to the CPPFLAGS environment variable. Do you have the corresponding libraries in /usr/local/lib? I also pasted detailed error output while configuring gromacs in SGI. ### checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... no checking dynamic linker characteristics... irix6.5 ld.so checking whether ln -s works... yes checking for sqrt in -lm... yes checking for fftw.h... no checking for sfftw.h... no configure: error: Cannot find any single precision fftw.h or sfftw.h Do you have single precision FFTW installed? If you are using packages, note that you also need fftw-devel to compile GROMACS. You can find the software at www.fftw.org, and detailed instructions at www.gromacs.org. If you compiled FFTW yourself: Note that the default FFTW setup is double precision. Change the FFTW configuration to single with --enable-float. If you want MPI support, use --enable-mpi. It is a good idea to install both single double. If your sysadm doesn't want to install it you can do it to a location in your home directory and provide the correct paths in .. ### With thanks ! B.Nataraj -- David. _ ___ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se +++ + ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm
Re: [gmx-users] configure problem in SGI
including the libfftw3.a and libfftw3f.a ? yea the above said both files, libfftw3.a and libfftw3f.a are there in /usr/local/lib. Do you use the csh or sh? I am using csh shell. With thanks ! B.Nataraj ___ -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - mmm... Fastmail... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] configure problem in SGI
Dear Mr.Eriv and Mr.spoel , Thanks for your help. Sorry for unnessary confusion caused, I just compared the version number as 3.0.1 , so I made mistake. Now again I tried to configure groamcs3.3 , Now a new problem has come up. The SGI which I am trying to install has its date setback for some other reason. So when I try to configure gromacs now, It shows following error. ### checking build system type... mips-sgi-irix6.5 checking host system type... mips-sgi-irix6.5 checking for a BSD-compatible install... config/install-sh -c checking whether build environment is sane... configure: error: newly created file is older than distributed files! Check your system clock ## Please give me suggestion to configure without changing the current date of the SGI. With thanks! B.Nataraj On Mon, 3 Apr 2006 10:35:50 +0200, Erik Lindahl [EMAIL PROTECTED] said: On Apr 3, 2006, at 10:28 AM, raja wrote: Dear Mr Erik, No, I use fftw-3.0.1 and gromacs-3.0.1 and more I have not selected FFTW-2 manually. Again, If you read the online installation instructions, it says quite explicitly that Gromacs-3.3 and later supports FFTW3. You are using an old Gromacs release with a new FFTW library. Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] configure problem in SGI
Dear Mr.Spoel, Thanks for your help. It worked now but during compilation, the following error occured . ## source='ghat.c' object='ghat.lo' libtool=yes \ DEPDIR=.deps depmode=sgi /bin/sh ../../config/depcomp \ /bin/sh ../../libtool --mode=compile --tag=CC cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/gromacs/share/top\ -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c -o ghat.lo ghat.c cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/gromacs/share/top\ -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c ghat.c -Wp,-MDupdate,.deps/ghat.TPlo -o ghat.o cc-1515 cc: ERROR File = ghat.c, Line = 233 A value of type int cannot be assigned to an entity of type real ***. gh = mk_rgrid(ix,iy,iz); ^ 1 error detected in the compilation of ghat.c. *** Error code 1 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) ## With thanks ! B.Nataraj On Mon, 03 Apr 2006 11:09:55 +0200, David van der Spoel [EMAIL PROTECTED] said: raja wrote: Dear Mr.Eriv and Mr.spoel , Thanks for your help. Sorry for unnessary confusion caused, I just compared the version number as 3.0.1 , so I made mistake. Now again I tried to configure groamcs3.3 , Now a new problem has come up. The SGI which I am trying to install has its date setback for some other reason. So when I try to configure gromacs now, It shows following error. ### checking build system type... mips-sgi-irix6.5 checking host system type... mips-sgi-irix6.5 checking for a BSD-compatible install... config/install-sh -c checking whether build environment is sane... configure: error: newly created file is older than distributed files! Check your system clock ## Please give me suggestion to configure without changing the current date of the SGI. restart from scratch set the date on the distribution files after unpacking to the current date on your machine using the touch command With thanks! B.Nataraj On Mon, 3 Apr 2006 10:35:50 +0200, Erik Lindahl [EMAIL PROTECTED] said: On Apr 3, 2006, at 10:28 AM, raja wrote: Dear Mr Erik, No, I use fftw-3.0.1 and gromacs-3.0.1 and more I have not selected FFTW-2 manually. Again, If you read the online installation instructions, it says quite explicitly that Gromacs-3.3 and later supports FFTW3. You are using an old Gromacs release with a new FFTW library. Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The professional email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error: relative constraint deviation after LINCS
Dear all, Thanks for your thoughts and suggestions. Please tell me how to update that patch,pme.c in already installed gromacs program. I mean to ask you whether I have to compile the gromacs again or is there easy way of adding pme.c patch file without recomipiling entire program. With thanks! B.Nataraj On Wed, 29 Mar 2006 08:32:54 -0800, David Mobley [EMAIL PROTECTED] said: Regarding the PME bug, I know I've said this before, but I think it would be a lot easier for people to find out about these things if there were a single page somewhere on the site that lists all of the known bugs with each version (and preferably their symptoms) and possibly also links to fixes. If I were a new user and just downloading 3.3 for the first time, I don't know how I would know that there is a bug with PME without searching the archives of the mailing list. Maybe even the 3.3 source available to download could be updated with patches every so often? Again, I'm just a bit nervous that people may be having problems due to *known bugs* in 3.3 simply because there is no easy way to find out about these bugs or their solutions. David On 3/29/06, David van der Spoel [EMAIL PROTECTED] wrote: Tom Joseph wrote: Curiously, what is pme_order set to in your mdp file? I experienced a very similar problem as you did when I had set pme_order to 6, and I don't know why... it's a known bug, please fetch the new pme.c from the ftp site. --Tom On Mar 28, 2006, at 10:28 PM, raja wrote: Hi gmxs, No reply yet for this posting, so I reposting the same error...Please give me the direction. With thanks ! B.Nataraj The Error part ## step 0 Step 10, time 0.02 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.002406 (between atoms 2664 and 2666) rms 0.90 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2664 2665 31.50.1090 0.1091 0.1090 step 30, will finish at Tue Mar 28 14:14:30 2006 Step 38, time 0.076 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.296349 (between atoms 2576 and 2577) rms 0.004434 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2576 2577 90.00.1090 0.1413 0.1090 2578 2579 90.00.1090 0.1180 0.1090 Step 39, time 0.078 (ps) LINCS WARNING relative constraint deviation after LINCS: max 4821.659668 (between atoms 2584 and 2585) rms 70.115692 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2557 2559 104.40.1450 0.5221 0.1449 2559 2560 87.20.1090 0.5446 0.1090 2559 2561 118.50.1530 0.5012 0.1529 2559 2572 99.80.1523 1.4141 0.1522 2561 2562 82.90.1090 0.0423 0.1090 2561 2563 69.90.1091 0.0341 0.1090 2561 2564 34.20.1529 0.0840 0.1529 2572 2573 88.10.1231 1.5691 0.1229 2572 2574 110.80.1335 6.8042 0.1335 2574 2575 106.00.1010 6.5640 0.1010 2574 2576 81.30.1456 8.8651 0.1449 2576 2577 41.10.1413 5.5404 0.1090 2576 2578 112.60.1532 12.6753 0.1529 2576 2588 100.30.1526 10.1017 0.1522 2578 2579 87.10.1180 54.2609 0.1090 2578 2580 92.40.1534 18.2981 0.1529 2578 2584 88.10.1538 35.5616 0.1529 2580 2581 89.10.1092 1.3620 0.1090 2580 2582 90.10.1090 1.4119 0.1090 2580 2583 88.10.1091 1.2295 0.1090 2584 2585 90.00.1090 525.6699 0.1090 2584 2586 91.50.1089 23.0823 0.1090 2584 2587 92.00.1089 22.9080 0.1090 2588 2589 104.30.1229 3.1250 0.1229 2588 2590 115.10.1335 2.8415 0.1335 2590 2591 109.10.1450 0.9337 0.1449 2590 2599 108.60.1450 0.9203 0.1449 2591 2592 112.40.1090 0.3062 0.1090 2591 2593 108.30.1529 0.2859 0.1529 2591 2602 120.10.1522 0.2576 0.1522 2593 2594 43.80.1090 0.1570 0.1090 2593 2595 45.30.1090 0.1562 0.1090 2596 2597 30.60.1090 0.1273 0.1090 2596 2598 41.20.1090 0.1451 0.1090 2596 2599 96.60.1529 0.1996 0.1529 2599 2600 133.40.1090 0.2447 0.1090 2599 2601 135.40.1090 0.2755 0.1090 2602 2603 32.10.1229 0.1593 0.1229 2602 2604 32.60.1335 0.1740 0.1335
Re: [gmx-users] Ligand moves out of box during EM steps
Dear Tsjerk , Thanks for your reply. Now I could retain the ligand in active site upto the stage of solvating it in the water box. Now to add counter ions, I run grompp and later added 10 Na+ counter ion to neutralize system using genion. At the output of genion, the ligand moved out to the corner, not only moved out , its atoms are distorted, If I tried to minimize at the same state , the whole system got minimized and ligand also restored to its original state(which mean bonds are all formed between the atoms). Now tell me whether those newly added counter ion will make a effect of this behaviour of shifting ligand to corner. And more is it right to neutralize the system without inclusion of ligand charge( Since ligand was not the part of the system while I was computing the charge of the system in pdb2gmx step). With thanks ! B.Natatraj On Thu, 23 Mar 2006 22:57:07 +0100, Tsjerk Wassenaar [EMAIL PROTECTED] said: Hi Raja, The protein.conf I took from your mail.., so that is whatever you did to get protein.conf! I think in your mail that was the structure obtained from pdb2gmx combined with the ligand. And what do you mean with the solvent box has shifted? I hoped the ligand would have shifted. If you use the same definition for the simulation cell, it couldn't have shifted, as it is defined from the origin, using the orthogonal components of the box vectors (first three numbers in the last line of the .gro file). If you meant that your ligand is now in the center of the box, nicely surrounded by the water and your protein is sticking out, that's ok. That was what I intended for you to obtain. That way, your ligand won't jump when you start to run your simulations. Hope it helps, Tsjerk On 3/23/06, raja [EMAIL PROTECTED] wrote: Dear Tsjerk Wassenaar, Thanks for your reply, Following your commands I could center ligand up in original position but the solvent box is shifted from its center... Please recheck the command you provided for me..since you have given as make_ndx -f protein.conf but where comes the file protein.conf in previous step. With thanks ! B.Nataraj On Thu, 23 Mar 2006 09:45:46 +0100, Tsjerk Wassenaar [EMAIL PROTECTED] said: Raja, Try: pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh pasting the ligand in make_ndx -f protein.conf editconf -f protein.conf -o protein.box -d 0.9 editconf -f protein.box -o protein.solv -c -n ... and select first the group corresponding to the ligand (for centering) and next the system (for output) genbox -cp protein.conf -cs -o protien.solv -p protein Tsjerk On 3/23/06, raja [EMAIL PROTECTED] wrote: Thanks for all your suggestions, But according to David mobley, I tried but no effect, the ligand still found at the corner with its atoms are in distorted condition. I use these commands : pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh Where protein with its ligand cut off. later I pasted the separate gro file for ligand as produced from PRODRG server into the protien.gro output from earlier command. editconf -f protein.conf -o protein.solv -d 0.9 genbox -cp protein.conf -cs -o protien.solv -p protein Now if I visulazie the output protein.solv.gro, the ligand is separated and located at corner. Though Alberto Malvezzi suggested to use SPDBV is good idea, but I want to accomplish this thing using GROMACS commands as suggested by David mobley,since it helps me to learn in depth what exactly gromacs editconf and genbox doing with protein. And more the reson why I do cut and paste the ligand in between pdb2gmx commands is the lack of RTP entry for my ligand is not updated in ffoplsa.rtp file. Simulatenusly I also work on building the proper RTP entry for the ligand of my interst. Right now I managed to produced ITP file for the ligand by PRODRG. Help is sorted from any of you as a script which make RTP format for ligand from its ITP file. With thanks ! B.Nataraj On Wed, 22 Mar 2006 07:57:29 -0800, David Mobley [EMAIL PROTECTED] said: If I remember correctly, the place where the coordinates of the protein get changed is the step involving genbox (or editconf), where it is translated to the center of the box. So an alternative approach to Alberto's suggestion is to combine the protein and the ligand *before* using editconf/genbox (but after doing pdb2gmx); I think then the ligand will still be placed correctly relative to the protein. I was using this approach at one point, with the additional benefit that you don't have to edit the coordinates using some other program. David On 3/22/06, Alberto Malvezzi [EMAIL PROTECTED] wrote: Hi Nataraj
[gmx-users] Req for script to make rtp entro of ligand with ffoplsa compatiable
Dear GMXIONS, Kindly provide me a script to make rtp entry for a ligand to use it for oplsa force field file. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access your email from home and the web ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Solvent accessbility of ligand in RNA
Dear GMXIONS, I have simulated RNA, and later docked ligand to the ensemble of average structure of RNA during some desired time steps. Now I wish to compute the solvent accessbility of ligand in the active site of a RNA. Is there a way within the gromacs to do it either directly or indirectly. If not within GROMACS , kindly give me the direction to do the same in any of publicaly avilable software. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Ligand moves out of box during EM steps
Dear GMXIONS, During the course of steps to simulation of ligand and enzyme complex, I have been struck at the level of minimization, due to inability of keeping my ligand at active site. I am using position restraints for all heavy atoms of protein,counter ions and for all atoms of my ligand, but still at the end of the minimization, the ligand goes out of the active site and end up locating itself just outside of the water box. How to check the position restrined protocol of my ligand really taken for consideration in energy minimization? and how to prevent my ligand from moving it from its initial position. With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Or how I learned to stop worrying and love email again ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Drug-Enzyme simulation
Dear GMXION, I already posted problem regarding drug-enzyme simulation using OPLSA ff for a drug whose topolgy computed from PRGDRG server. But no solution yet to me. I absolutly followed each steps of drug-enzyme simulation tutorial of GMX, in addition I also played around ffoplsaa.atp, ffoplsaanb.itp ffolpsaa.rtp files under share folder as per various mails found in GMX user list but there is no use. Still I am getting error in grompp step prior to em run. Error output --- Program grompp, VERSION 3.3 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'CR61' not found! --- Where 'CR61' is the first atom type of drug as listed in drg.itp for my drug, produced by PRGDRG server. Yours help is very much needed ! With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error : Molecule type redefined
Dear GMXION, In a run for drug-enzyme simulation, the grompp run prior to em , shows the following error --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 887 Fatal error: moleculetype PN1 is redefined --- Where PN1 is the name of the drug, whose topology defined in DRG.itp file and the file is included in protein.top file. If I remove PN1 under [moleculetype] in any one of the file,either in DRG.itp or protein.top, it works but showing different error of mismatch coordinate between protein.top and protein.gro file as expected. What is the solution ? With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - mmm... Fastmail... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to make drug for OPLSA ff compatiable
Dear GMXion, I am now persuing simulation of drug-enzyme complex. I made topology and gro file for drug using PRGDRG server. I am using OPLSA force field for simulation since my protein having Fe(II) at active site. I followed all steps based on drug-enzyme simulation tutorial of gmx. But still it shows error in grompp step for drug's atom types not found. I also updated the missing atom types of drugs in ffoplsaa.itp, ffoplsaanb.itp in share/top folder. but still the run shows the same error for new atom types in drug.itp file. Any straight forward solution for this ? With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - The way an email service should be ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
