Dear Rebeca, I modestly build a program based on antechamber and inspired mostly by amb2gmx.pl:
http://code.google.com/p/acpypi/ I hope it can be a bit easier to use. You should also take a look in the tutorials I put there, because the may give you an idea why you are facing problems (I suspect your lipid.itp is in the wrong place of the top file). And it also may help you to better set up ffamber in Gromacs. Moreover, it seems you're using amber atom types instead of gaff atom types (did you use antechamber right?). I would suggest you to use gaff atom type. Or try just to delete the [ atomtypes ] field and pray that the ffamber## ff you took in GROMACS will handle it. Cheers, Alan On Thu, Jul 31, 2008 at 7:34 PM, <[EMAIL PROTECTED]> wrote: > > Hello, > I am trying to translate the amber topology for a system membrane+protein > (dry) to Gromacs. In view of the problems caused in amb2gmx.pl due to the > size of the system (more than 600.000 atoms) I had tried another alternative: > I created the amber topology for the protein and for a unique lipid molecule > separately and I converted them to gromacs using amb2gmx.pl (now, no problems > were found, as is logic). Then, from the gromacs topologies, I construct the > .itp files for the protein and lipid, removing the correspondent lines and > putting them into another file that I have called amberff.itp > > However, several atomtypes for the lipid are the same than those for the > protein, and they have nothing to do between them: > > [ atomtypes ];name bond_type mass charge ptype sigma > epsilonO O 0.0000 0.0000 A 2.95992e-01 8.78640e-01H1 > H1 0.0000 0.0000 A 2.64953e-01 6.56888e-02N3 N3 > 0.0000 0.0000 A 3.25000e-01 7.11280e-01O2 O2 0.0000 > 0.0000 A 2.95992e-01 8.78640e-01HA HA 0.0000 0.0000 A > 2.64953e-01 6.56888e-02HC HC 0.0000 0.0000 A > 2.64953e-01 6.56888e-02C C 0.0000 0.0000 A 3.39967e-01 > 3.59824e-01CT CT 0.0000 0.0000 A 3.39967e-01 > 4.57730e-01HP HP 0.0000 0.0000 A 2.64953e-01 6.56888e-02 > > and I am getting errors in grompp due to this fact. > > Does anybody has any idea to solve this? > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< _______________________________________________ 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
