Dear Vivek, you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs. nahren
--- On Tue, 8/12/08, vivek sharma <[EMAIL PROTECTED]> wrote: From: vivek sharma <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Tuesday, August 12, 2008, 6:34 PM Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel <[EMAIL PROTECTED]> vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command.... pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error..... ....... ....... ....... ........ N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom ------------------------------------------------------- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens ------------------------------------------------------- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. You have an incorrect pdb file. An atom is missing. You have to fix it yourself. With thanx, Vivek ------------------------------------------------------------------------ _______________________________________________ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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