Thanks Justin Indeed, It worked !!!
In french, one says: "je ne dormirai pas idiot ce soir". Stéphane >Thank you Roland for your response >I have effectively downloaded from the >http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version >of gmx Unfortunately, the unpacked directory does not contain a >configure file, I have only an configure.ac. >So my question is: how to obtain a fully fonctional version of 4.1 >without using git >Thank you for your response > > Hi, > > there is currently no web-interface on the official git server. Thus > repo.or.wz is probably the best solution. > I checked that http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is > up-to-date. > > Roland > > On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950 <[email protected]>wrote: > > >> Hi all, >> >> >> >> For a future project, I would like to use gromacs for simulations with the >> CHARMM force field. I am aware that the CHARMM ff is not yet "officially" >> supported by gromacs, even if a paper about this port will be published >> soon. By reading the mailing list, I understand that a beta version of >> gmx4.1 is available for testing from the git depositary. I have tried to use >> git, but since I am behind a firewall, I cannot easily access to the >> depositary. I have tried to obtain a previous from >> http://repo.or.cz/w/gromacs.git through the master branch but I am not >> sure that the file downloaded was the latest version. Therefore, my question >> is how to obtain the latest version of pre gmx4.1 without using git ? >> >> >> >> Thank you for your help >> >> >> >> Stéphane >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> > > > > ------------------------------ Message: 3 Date: Tue, 26 Jan 2010 14:00:00 -0500 From: "Justin A. Lemkul" <[email protected]> Subject: Re: [gmx-users] Re: Obtain a pre-version of gromacs 4.1 without git To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=windows-1252; format=flowed Stephane Abel wrote: > Thank you Roland for your response > > I have effectively downloaded from the > http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version > of gmx Unfortunately, the unpacked directory does not contain a > configure file, I have only an configure.ac. > > So my question is: how to obtain a fully fonctional version of 4.1 > without using git > In the code you downloaded, there should be a script called "bootstrap" which you can execute to generate the configure file. -Justin > Thank you for your response >> >> Hi, >> >> there is currently no web-interface on the official git server. Thus >> repo.or.wz is probably the best solution. >> I checked that http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is >> up-to-date. >> >> Roland >> >> On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950 >> <[email protected]>wrote: >> >> >>> Hi all, >>> >>> >>> >>> For a future project, I would like to use gromacs for simulations >>> with the >>> CHARMM force field. I am aware that the CHARMM ff is not yet >>> "officially" >>> supported by gromacs, even if a paper about this port will be published >>> soon. By reading the mailing list, I understand that a beta version of >>> gmx4.1 is available for testing from the git depositary. I have tried >>> to use >>> git, but since I am behind a firewall, I cannot easily access to the >>> depositary. I have tried to obtain a previous from >>> http://repo.or.cz/w/gromacs.git through the master branch but I am not >>> sure that the file downloaded was the latest version. Therefore, my >>> question >>> is how to obtain the latest version of pre gmx4.1 without using git ? >>> >>> >>> >>> Thank you for your help >>> >>> >>> >>> Stéphane >>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >> >> >> >> > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 4 Date: Wed, 27 Jan 2010 08:09:47 +1100 From: "Dallas B. Warren" <[email protected]> Subject: RE: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" So, what EXACTLY are you doing? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of vivek sharma Sent: Monday, 25 January 2010 7:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial HI Tsjerk, Thanks for your reply. But, I can't see if it is going suddenly or gradually. What i can see is the ligand is away from the molecule after editing the gro file with PRODRG output. It seems liek PRODRG has modified the co-ordinates that places ligand away from the protein. ~Vivek 2010/1/25 Tsjerk Wassenaar <[email protected]> Hi Vivek, > Now when I am processing the modified .gro file to generate box, the ligand > and cofactor are going away from the protein molecule and I am not able to > analyze the complex. Gradually going away, or suddenly jumping? In the latter case, read up on periodic boundary conditions. Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100127/41f072dc/attachment-0001.html ------------------------------ Message: 5 Date: Tue, 26 Jan 2010 16:26:09 -0500 From: Miguel Quiliano Meza <[email protected]> Subject: [gmx-users] the solvent group SOL is not continuous To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" *Hi everyone. I have a problem when I try to run GENION, GROMACS says: * WARNING: turning of free energy, will use lambda=0 Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision) Using a coulomb cut-off of 0.9 nm Will try to add 0 Na ions and 15 NA+ ions. Select a continuous group of solvent molecules Opening library file /usr/share/gromacs/top/ aminoacids.dat Group 0 ( System) has 275439 elements Group 1 ( Protein) has 1722 elements Group 2 ( Protein-H) has 1371 elements Group 3 ( C-alpha) has 185 elements Group 4 ( Backbone) has 555 elements Group 5 ( MainChain) has 741 elements Group 6 (MainChain+Cb) has 909 elements Group 7 ( MainChain+H) has 921 elements Group 8 ( SideChain) has 801 elements Group 9 ( SideChain-H) has 630 elements Group 10 ( Prot-Masses) has 1722 elements Group 11 ( Non-Protein) has 273717 elements Group 12 ( ZN) has 1 elements Group 13 ( SOL) has 273702 elements Group 14 ( LIG) has 14 elements Group 15 ( Other) has 273717 elements Select a group: 13 Selected 13: 'SOL' ------------------------------------------------------- Program genion, VERSION 3.3.3 Source code file: ../../../../src/tools/gmx_genion.c, line: 429 Fatal error: The solvent group SOL is not continuous: index[9]=1732, index[10]=1747 ------------------------------------------------------- "Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is." (Jackie Brown) *I do not know the reason,the number of residues in top file and pdb file are the same. The only warning that I saw was when I ran grompp: * WARNING 1 [file 1x8a.top, line unknown]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2 NH, OH, CO2, CO, etc. *Coincidentally they are some of the atomos of my ligand* * I have been reading the web and no-one says nothing about it. I would be very grateful if someone can help me or give me advices. Best Regards MIguel Quiliano* -------------- next part -------------- An HTML attachment was scrubbed... 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