You need to create your topology file manually and have a look at this: http://wiki.gromacs.org/index.php/Exotic_Species
> -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of RAJAVARMAN.K > Sent: 09 May 2008 15:34 > To: [email protected] > Subject: [gmx-users] pdb2gmx > > Respected sir, > > am working with gold cluster .am planing to simulate > gold cluster in the presence of vacuum.but i can,t able to convert the pdb > file into gro,top format caz of the following statement" Residue '2' not > found in residue topology database ". > > i already gone through gromacs mailing list as well as > gromacs manual 5 chapter.but i really don't know what to change in .rtp,.top > files. so plz help me .am attaching my error statement as well as input > file.already have experience in working with protein,peptides,domain.but > this is first time am using metal cluster ( i.e 40 atoms of gold).can u > please kindly help me by creating gold cluster topology,gro file. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ 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
