jagshemash (hi) Mohammed, OK there are two ways of dealing with this: 1. You add water with genbox ....run grommpp ..then feed in the resulting *tpr file into genion...genion replaces a water molecule with a pre-selected appropriate ion ("genion -h" should give you the help menu). However, you must remember to #include ions.itp in your *top file. If for some reason you don't want water in your system 2. You just manually put a K+ ion in yourself but need to define it in your own itp something like this should do..if u copy it into a ascii file. [ moleculetype ] ; name nrexcl K 1 [ atoms ] ; id atype resnr resname aname cgnr charge mass 1 K+ 1 K K 0 1.000 22.9898 cheers Kia > > Message: 3 > Date: Thu, 9 Nov 2006 11:55:57 -0600 > From: "Mohamed Osman" > Subject: [gmx-users] pdb2gmx with force field option > To: gmx-users@gromacs.org > Message-ID: > <5de0a28d0611090955s47976acdl9c89dd0139d8bb1c@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > As my first Gromacs simulation I am trying to simulate a protein with K+ > ion. > When I use pdb2gmx with GROMACS96 43a2, it complains about the K+ ion and > does not generate the topology file. > > When I remove the K+ ion, I get a topology file, but I need the K+ for the > simulation. Can I add the K+ ions at the end of the .gro files and proceed? > > > 1. How can I run pdb2gmx and tell it to look for the force filed information > for K in a different file? I tried -ff but got unclear message? > > 2. When I searched in the share/top directrory I found that each force > field name with several extensions:.itp, .dhb and .atp. I only have a > K.itpfile, is that enough? > > > 3. To insert the protein into a lipid I used genbox command: > genbox -cp protein.pdb -cs lipid.pdb > > The protein sinks deep into the lipid and I need to shift the protein back > up? What is the best to do it without overlapping with the solvent > molecules? > > 4. What is a better way of doing step 3? > > > Thanks > > Mohamed Osman > Professor of Electrical Engineering > Washington State University -- 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)