Re: [gmx-users] NBFIX to gromacs

2012-05-03 Thread Ricardo O. S. Soares
gt;> >> >> >____ >> > De: Peter C. Lai >> >Para: Discussion list for GROMACS users >> >Enviadas: Segunda-feira, 30 de Abril de 2012 20:46 >> >Assunto: Re: [gmx-users] NBFIX to gromacs >> > >> >

Re: [gmx-users] NBFIX to gromacs

2012-05-02 Thread Peter C. Lai
to KJ and Angstrom to > nm, adapt and append to [ pairtypes ]. Could this be the right move? > Thanks again, > > Ricardo. > > > > > > > > > > De: Peter C. Lai > >Para: Discussion list for GROMACS users &g

Re: [gmx-users] NBFIX to gromacs

2012-05-02 Thread Ricardo O. S. Soares
ai >Para: Discussion list for GROMACS users >Enviadas: Segunda-feira, 30 de Abril de 2012 20:46 >Assunto: Re: [gmx-users] NBFIX to gromacs > >NBFIXes haven't been used in charmm for a long time (1998), although >current versions still read topologies containing those recor

Re: [gmx-users] NBFIX to gromacs

2012-04-30 Thread Peter C. Lai
NBFIXes haven't been used in charmm for a long time (1998), although current versions still read topologies containing those records. Perhaps you should reparameterize your molecule with a more current version? (Or start with the coordinate file and use pdb2gmx with the converted ff). The only th

[gmx-users] NBFIX to gromacs

2012-04-30 Thread Ricardo O. S. Soares
Hello GMX users, does anyone that dealt with Charmm before knows how to translate the NBFIX section into a Gromacs ff format? After convertion from KCal to KJ, does it go into [pairtypes]? I see that it concerns to corrections in LJ interactions, however the charmm documentation seems a bit unc