Hi Following on from Mark's comments, if you want to get rid of water and ion molecules then just delete them in a text editor but bear in mind that renumbering is not an issue as editconf will do this for you!!!! If you are planning to make a movie (I had a first year graduate student asking this last week worded in the same way as you! :)), then use VMD google "VMD" and you can easily download it: load ur pdb/gro file click on it (highlight it) then load data into molecule click on graphics then representations then just type protein (make another rep.) and type resname XXXX (the particular lipid you are using) cheers Kia > > Message: 8 > Date: Tue, 26 Sep 2006 01:37:43 +1000 > From: Mark Abraham > Subject: Re: [gmx-users] How can I remove water and ion molecules > To: Discussion list for GROMACS users > Message-ID: <4517F7C7.5050305@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > jahanshah ashkani wrote: > > Hi, > > How can I remove water and ion molecules from the pdb file after energy > > minimization and molecular dynamic simulation? > > From a pdb file is easy - just get a text editor and delete those > lines. Never mind about the atom or residue numbering. > > Is this the question you meant to ask? > > Mark > > -- Kia Balali-Mood PhD, CBiol, MIBiol Postdoctoral Research Associate, Department of Biochemistry, Oxford University, OX1 3QU, UK sansom.biop.ox.ac.uk/kia/ , tel. +44 (0)1865 275 (380 or 275)