Hi all, maybe these are stupid questions, but in the moment I'm a bit in a files' mess, so I apologize for that...
I want to use a lipid bilayer pdb from the Tieleman group, let's say http://moose.bio.ucalgary.ca/files/dppc64.pdb, and the first goal is to get the structure "into" GROMACS and to see if it works. If I run pdb2gmx -ignh -ff G53a6 -f dppc64.pdb -o lipids.pdb -p lipids.top I get a problem with the rtp file, "Atom N4 in residue DPPC 1 not found in rtp entry with 50 atoms while sorting atoms", , but it works with gmx, so 1) may I just replace the [DPPC] part of ffG53a6.rtp with the equivalent part of ffgmx.rtp or have I to edit the G53a6 file so that the first columns are the same? It works with the gmx force field and I can run editconf and genbox. But when I use grompp_d -f em.mdp -c lipids_b4em.pdb -p lipids.top -o lipids_em.tpr the program is determined by too many warnings like "WARNING 1 [file "lipids_A.itp", line 69]: No default Bond types, using zeroes" so I think, this is the place, where the itp files (lipid.itp, dppc.itp), offered besides the pdb should do some job here. But 2) how will I get these files involved into my simulation? I hope, you understand my problem, as for myself it is not yet really clear, what e.g. the itp file will actually do within the process... Best Volker -- ################################### Volker Wirth Center for Medical Physics and Technology Biophysics Group FAU Erlangen-Nuremberg Email: vwirth%at%biomed.uni-erlangen.de ################################### _______________________________________________ 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
