[gmx-users] [Fwd: TFE 33%]
Please keep these requests on the mailing list, so that others might be able to answer your question better than I, and that the answer can be found by others later. Mark Original Message Subject:TFE 33% Date: Sat, 17 Feb 2007 08:55:08 -0800 (PST) From: kourosh bamdad [EMAIL PROTECTED] To: [EMAIL PROTECTED] Dear prof. ABRAHAM its more than 10 days that i've been dealing with a simple simulation using a TFE SPC for my solvent box but i stopped every time at the (steep or em.mdp) stuff all the time. It send me this message: number of coordinates in coordinate file does not match topology ( .pdb, top 0) what should i do to over this step? do i need to change .top file whith something? or the error backs to the steep or em.mdp stuff? Thanks Be a PS3 game guru. Get your game face on with the latest PS3 news and previews at Yahoo! Games. http://us.rd.yahoo.com/evt=49936/*http://videogames.yahoo.com ___ 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] [Fwd: TFE 33%]
i've been dealing with a simple simulation using a TFE SPC for my solvent box but i stopped every time at the (steep or em.mdp) stuff all the time. It send me this message: number of coordinates in coordinate file does not match topology ( .pdb, top 0) what should i do to over this step? do i need to change .top file whith something? or the error backs to the steep or em.mdp stuff? Thanks Please describe your problem fully... at the (steep or em.mdp) stuff doesn't help anybody work out your problem, and makes them not want to help you. When you want free help, you have to work at making it easy for someone to give it to you. If you're paying them, then do whatever you like :-) Nonetheless, it is clear that you have made an error with the formatting of your .top file. Read chapter 5 carefully and then see where your .top file doesn't satisfy the format described. Alternatively, start again with a .top file that does work for just water, and work in the TFE again. 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] [Fwd: TFE 33%]
Hi Specify exact number of TFE and Water present in your *.pdb file to *.top file..also specify *.itp of TFE in the top file... Chiradip --- Mark Abraham [EMAIL PROTECTED] wrote: i've been dealing with a simple simulation using a TFE SPC for my solvent box but i stopped every time at the (steep or em.mdp) stuff all the time. It send me this message: number of coordinates in coordinate file does not match topology ( .pdb, top 0) what should i do to over this step? do i need to change .top file whith something? or the error backs to the steep or em.mdp stuff? Thanks Please describe your problem fully... at the (steep or em.mdp) stuff doesn't help anybody work out your problem, and makes them not want to help you. When you want free help, you have to work at making it easy for someone to give it to you. If you're paying them, then do whatever you like :-) Nonetheless, it is clear that you have made an error with the formatting of your .top file. Read chapter 5 carefully and then see where your .top file doesn't satisfy the format described. Alternatively, start again with a .top file that does work for just water, and work in the TFE again. 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 Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA ___ Inbox full of unwanted email? Get leading protection and 1GB storage with All New Yahoo! Mail. http://uk.docs.yahoo.com/nowyoucan.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
