<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear Mr. Peter C. Lai,</div><div><br></div><div>I appreciate your kind response.</div><div><br></div><div>I apologize for the delay on my part.</div><div>This NBFIX parameters that I'm working with came from the str file in http://terpconnect.umd.edu/~jbklauda/research/download/chol_new.str , which dates from 2012.</div><div>I successfully converted this whole file, now I'm wondering about this NBFIX section.</div><div>I'm thinking about converting these values from Kcal to KJ and Angstrom to nm, adapt and append to [ pairtypes ]. Could this be the right move?</div><div>Thanks again,</div><div><br></div><div>Ricardo.<br></div><div><br></div><br><div><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; margin-top: 5px; padding-left: 5px;"> <div style="font-family: times new roman, new york,
times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">De:</span></b> Peter C. Lai <pcl@uab.edu><br> <b><span style="font-weight: bold;">Para:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Enviadas:</span></b> Segunda-feira, 30 de Abril de 2012 20:46<br> <b><span style="font-weight: bold;">Assunto:</span></b> Re: [gmx-users] NBFIX to gromacs<br> </font> </div> <br>NBFIXes haven't been used in charmm for a long time (1998), although <br>current versions still read topologies containing those records. Perhaps you <br>should reparameterize your molecule with a more current version? (Or start with<br>the coordinate file and use pdb2gmx with the converted ff). The only thing I<br>can think of if you really need to do it is to
create new atom types.<br>As far as I know, gromacs only supports 1 set of vdw coefficients and a 1-4<br>pair.<br><br><br><br>On 2012-04-30 01:30:59PM -0700, Ricardo O. S. Soares wrote:<br>> Hello GMX users,<br>> <br>> 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]?<br>> I see that it concerns to corrections in LJ interactions, however the charmm documentation seems a bit unclear to me.<br>> <br>> Thanks again,<br>> Ricardo.<br><br>> -- <br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a
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