Re: [gmx-users] genbox give coord file more waters than top file
8 mar 2007 kl. 01.32 skrev Mark Abraham: Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? genbox doesn't read a top and produce that many solvent molecules. For a start, how does it know what shape you want them in? Read man genbox, choose what you want to do, apply genbox, and then edit your .top so the number of waters agrees with what genbox produced... not the other way around. Mark I'm not so sure about that. genbox *does* take a top file as an optional argument. genbox -h tells me: Finally, genbox will optionally remove lines from your topology file in which a number of solvent molecules is already added, and adds a line with the total number of solvent molecules in your coordinate file. I have never used this option, so I don't know exactly how it works, but I expect it to do what William wants it to do. ___ 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 ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ 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] genbox give coord file more waters than top file
From: WILLIAM R WELCH [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] genbox give coord file more waters than top file Date: Wed, 07 Mar 2007 16:53:11 -0600 Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? I have seen this problem for the first time on our Gromacs workshop last week. I think the problem is that genbox does not recognize some crystal waters in your input coordinate file. genbox currently checks for SOL, WAT and HOH. What is the residue name of your crystal waters? The solution for the moment is to manually count the water molecules in the gro file and then correct the top file. Berk. _ Live Search, for accurate results! http://www.live.nl ___ 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] genbox give coord file more waters than top file
8 mar 2007 kl. 01.32 skrev Mark Abraham: Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? genbox doesn't read a top and produce that many solvent molecules. For a start, how does it know what shape you want them in? Read man genbox, choose what you want to do, apply genbox, and then edit your .top so the number of waters agrees with what genbox produced... not the other way around. Mark I'm not so sure about that. genbox *does* take a top file as an optional argument. genbox -h tells me: Finally, genbox will optionally remove lines from your topology file in which a number of solvent molecules is already added, and adds a line with the total number of solvent molecules in your coordinate file. I have never used this option, so I don't know exactly how it works, but I expect it to do what William wants it to do. Maybe this works, I've never used it either... but the point is that the source of the information about how many waters to add comes from the genbox command line, not this .top file. I think William wanted the number of waters in his .top file to be added to his .gro file, and this is an ill-defined proposition. 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
Re: [gmx-users] genbox give coord file more waters than top file
From: Mark Abraham [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] genbox give coord file more waters than top file Date: Thu, 8 Mar 2007 22:27:01 +1100 (EST) 8 mar 2007 kl. 01.32 skrev Mark Abraham: Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? genbox doesn't read a top and produce that many solvent molecules. For a start, how does it know what shape you want them in? Read man genbox, choose what you want to do, apply genbox, and then edit your .top so the number of waters agrees with what genbox produced... not the other way around. Mark I'm not so sure about that. genbox *does* take a top file as an optional argument. genbox -h tells me: Finally, genbox will optionally remove lines from your topology file in which a number of solvent molecules is already added, and adds a line with the total number of solvent molecules in your coordinate file. I have never used this option, so I don't know exactly how it works, but I expect it to do what William wants it to do. Maybe this works, I've never used it either... but the point is that the source of the information about how many waters to add comes from the genbox command line, not this .top file. I think William wanted the number of waters in his .top file to be added to his .gro file, and this is an ill-defined proposition. Mark This depends. If the gro and top came out of pdb2gmx, pdb2gmx already recognized the water molecules and wrote the gro and top files. genbox is supposed to regonize these crystal waters in the gro and top file. Normally it would just add a line for the added water molecules. But genbox is so smart that it checks if the waters in the output configuration match the number in the orginal top plus the added waters, and it corrects the top if there is something wrong. I would guess that this is where the error occurs. Please file a bug report to bugzilla.gromacs.org with the gro and top file and the command line used for genbox. Berk. _ FREE pop-up blocking with the new Windows Live Toolbar - get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ ___ 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] genbox give coord file more waters than top file
Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? genbox doesn't read a top and produce that many solvent molecules. For a start, how does it know what shape you want them in? Read man genbox, choose what you want to do, apply genbox, and then edit your .top so the number of waters agrees with what genbox produced... not the other way around. 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
