[gmx-users] Re: Problems prior to running lipid-protein simulation
[EMAIL PROTECTED] wrote: Bruce Milne wrote: > You don't have to run pdb2gmx for the whole system at any point Probably true. > (it's > not going to work anyway unless you add the POPC parameters to all the > force field files and then add the POPC residue to the .rtp file so > that pdb2gmx can recognize it). Not quite true. The contents of the .itp files don't matter to pdb2gmx since it writes a .top file that #includes them. So you need to have a working POPC entry in an .rtp file for pdb2gmx, and later on, when using grompp, you'll need the former contents of the .rtp file to correspond to stuff the .itp files. The latter you need even without using pdb2gmx, of course. Good point. I was only considering the case where you want pdb2gmx to provide you with a complete .top file that needs no additions and takes all its parameters from the same place (as you would get for a protein for example). Anyway, if you have the .itp files then I think it is easier to simply add the required #include lines to the protein.top file so that it covers all the molecule types in your coordinate file without trying to get pdb2gmx to recognize the lipids. Cheers, Bruce -- "Hamewith - the road that's never dreary" Dr. Bruce F. Milne CEQOFFUP Faculdade de Farmácia Universidade do Porto Rua Aníbal Cunha - 164 4050-047 Porto Portugal email: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] Re: Problems prior to running lipid-protein simulation
Bruce Milne wrote: You don't have to run pdb2gmx for the whole system at any point Probably true. (it's not going to work anyway unless you add the POPC parameters to all the force field files and then add the POPC residue to the .rtp file so that pdb2gmx can recognize it). Not quite true. The contents of the .itp files don't matter to pdb2gmx since it writes a .top file that #includes them. So you need to have a working POPC entry in an .rtp file for pdb2gmx, and later on, when using grompp, you'll need the former contents of the .rtp file to correspond to stuff the .itp files. The latter you need even without using pdb2gmx, of course. Mark ___ gmx-users mailing listgmx-users@gromacs.org 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
[gmx-users] Re: Problems prior to running lipid-protein simulation
Dear Adak, [EMAIL PROTECTED] wrote: Dear All; when I try to run pdb2gmx command for making .top file of POPC+Protein, an error appears: Residue 'POPC' not found in residue topology database. I have copied all necessary .itp files in share folder and also in the path where it is run. what could be the problem and how to solve it? (I have passed these steps long time ago but now I am not able to reproduce the procedure!) thanks; Adak Nasiripour. I think the process you might be wanting to perform is to run pdb2gmx for your protein only (with suitably adjusted coordinates so that it matches your bilayer coordinates) and then add #include lines to the resulting topology to add in the POPC part *after* the force field #include statement: #include "ffgmx.itp" #include "lipids.itp" #include "popc.itp" - assuming that these are your .itp file names. Then adjust the [ molecules ] section to list the number and type of your components and you should have a working .top file. You don't have to run pdb2gmx for the whole system at any point (it's not going to work anyway unless you add the POPC parameters to all the force field files and then add the POPC residue to the .rtp file so that pdb2gmx can recognize it). Cheers, Bruce -- "Hamewith - the road that's never dreary" Dr. Bruce F. Milne CEQOFFUP Faculdade de Farmácia Universidade do Porto Rua Aníbal Cunha - 164 4050-047 Porto Portugal email: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org 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
