Thank you for your advice! I reformatted the ffG43a2x.hdb file, but now pdb2gmx is complaining about the ffG43a2x-n.tdb file, that is different from the ffG53a6 one, and probably it would complain also for ffG43a2x-c.tdb. Here, also the fields gd_* don't match. Is there the way to use the existing topologies with another gromos force field instead of reformatting all the ffG43a2x* files? What about the "atomtype 'CA' not found!" error?
On Fri, Mar 21, 2008 at 12:57 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting Chiara Parravicini <[EMAIL PROTECTED]>: > > > Dear gromacs users, > > > > I would like to perform simulations of a protein embedded in popc, > using a > > force field of the gromos series and I downloaded popc.pdb, popc.itp, > > lipid.itpa and the force field ffG43a2x extended for lipids. > > Looking throughout the archive I found different suggestions, but none > of > > them help me to successfully perform my simulations: > > > > - Using the ffG43a2x* force field, when I run pdb2gmx on the popc.pdb, I > get > > this error: > > > > Fatal error: > > > > Error in hdb file ffG43a2x.hdb: > > > > Wrong number of control atoms (2 iso 3) on line: > > > > 1 1 N -C CA > > Right; I think the format of the .hdb file changed somewhere along the > way, and > ffG43a2x is formatted in the old style. What pdb2gmx is complaining about > is > that it thinks it is trying to add an atom named 'N', with reference atoms > of > -C and CA. Compare the ffG43a2x.hdb with, say, ffG53a6.hdb, and you will > see > the difference. The first atom specified must be the name of the hydrogen > atom > you wish to add, so that line should be something like: > > 1 1 H N -C CA > > For more on .hdb files, read the manual, section 5.5.2. > > -Justin > > > > > - If I manually write a topology file for the ffG43a2x force field and > > submit it to grompp to write a .tpr, I get this error: > > > > Fatal error: > > Atomtype 'CA' not found! > > > > In the topology file I included both lipid.itp and popc.itp, and I > > commented the following lines in the lipid.itp file as suggested: > > > > [ defaults ] > > > > 1 1 > > > > - I also tried to add the different sections [ atomtypes ], [ pairtypes > ], > > etc... of the lipid.itp files to ffG53a5* files, but I still get the > error: > > > > Atomtype 'CA' not found! > > > > Does anybody know what I miss? Is there a way to resolve this problem > and > > use popc with ffG53a5 or ffG43a2x? > > > > All comments are very appreciated! > > Thanks in advance! > > > > Chiara > > > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-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 >
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