Hi Maite, Indeed you shouldn't really run the lipids through pdb2gmx, but try to obtain a .itp file for a lipid, matching the force field you're trying to use. What you can do is take one lipid and run it through pdb2gmx, using your favourite force field. Make sure that the resulting structure file is not different in terms of the number of atoms and the order of them. Then you can use #include "lipid_ffG53a5.itp" in your .top file and under system list the number of lipids you have in your structure file. It may be a good idea to edit the lipid_ff53a6.itp file and change the name of the molecule. I hope I'm a bit clear, but in case I'm not, I think that you have to do additional reading of the manual in order to understand the topology files (chapter 5) until you grasp the idea. Now, to summarize a bit:
1. Construct the topology for your protein using pdb2gmx+ffG53a5 2. Extract one lipid from lipid.pdb and run it through pdb2gmx+ffG53a5 3. Modify the resulting .top file from #2 to make it a .itp file (a molecule definition) 4. Set up the system consisting of the protein and the lipids (and make sure that all the lipids are whole, i.e. not split over the periodic boundaries) 5. construct the topology for the system by adding the lipid topology to the protein.top file. Hope it helps, Tsjerk On 3/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
maite lopez wrote: > i've changed the atoms of the dppc.itp file by the atoms of the DPPC > molecule that appear in the ffG53a5.rtp file (for example LC3 by CH3) > and run grompp , but it gives : > Fatal error: > Atomtype 'C1' not found! > > I don´t know how to convert my lipids to ffG53a5. Could you > explain me briefly? So find where C1 is being referenced, and whether it should be being defined elsewhere, and if it isn't defined work out why it isn't. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
-- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
