Dear Leila Ok,But you have to separate your ions from your general pdb file(protein+ions) in the form of pdb, in the other words you need to obtain the pdb files for your ions separately and then paste it to PRODRG server.because your protein has more than 300 atoms alonly. I hope it can help you
On Sat, Oct 16, 2010 at 12:00 PM, leila karami <karami.lei...@gmail.com>wrote: > Dear mohsen ramezanpour* * > > yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make > topology file but > > ERRDRG> Too many atoms in this molecule (should be <=300). > PRODRG> Program terminated unsuccessfully, sorry! > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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