Hi Justin, Thanks for the advice. I solved my problem by just including the charmm27.ff forcefield itself at the top of the topol.top file (and deleting the default line) I guess that with this change i’m adding the atomtype OW into the topology file. I’m going to follow your advices respect to what water model should i use. Cheers,
-- Carlos Navarrro Retamal Ingeniero en Bioinformática Estudiante de doctorado en Ciencias Aplicadas, Universidad de Talca, Chile Centro de Bioinformática y Simulación Molecular(CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 798, Fax: 56-71-201 561 Email: carlos.navarr...@gmail.com o cnava...@utalca.cl On Tuesday, April 8, 2014 at 4:30 PM, Justin Lemkul wrote: > > > On 4/8/14, 11:18 AM, Carlos Navarrro Retamal wrote: > > Hello everyone, > > I'm trying to perform a MD of a mixture of solvent (in my case > > glycerol+water). > > In order to do that i first obtained the parameters of glycerol on CHARMM > > on here -> par_all36_carb.prm. To use this parameters on gromacs i used the > > psf2topol.py script ->https://github.com/resal81/PyTopol, generating a .top > > and a .itp file respectively. > > Just to try these files, i create a box with 2 molecules of glycerol and > > add 106 water molecules (SPC)-> Gly_solv.gro file. > > Finally, when i edit the topol.top file i add the next line: #include > > "charmm27.ff/spc.itp", to include the parameters of the SPC water model, > > but when i run grommp to make a minimization of the system i got the next > > error message: > > > > > Fatal error: > > > Atomtype OW not found > > > For more information and tips for troubleshooting, please check the > > > GROMACS > > > website at http://www.gromacs.org/Documentation/Errors > > > > > > > but if i remove the water (and of course the include line into the > > topol.top file) grommp works just fine :/ > > I really don't know what may be happening. > > > > > In theory, the CHARMM27 files that come with Gromacs can support SPC, but in > practice, there is no reason for you to do it. CHARMM force fields are > parametrized for use with TIP3P; other water models risk invalidating the > force > field. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu (mailto:jalem...@outerbanks.umaryland.edu) > | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org (mailto:gmx-users-requ...@gromacs.org). > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
