<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-size: 12pt; "><span>Dear Mr. Lai,</span></div><div style="font-size: 12pt; "><span><br></span></div><div style="font-size: 12pt; "><span>I see. I'll look more deeply into it, thanks for your answer.</span></div><div style="font-size: 12pt; "><span><br></span></div><div style="font-size: 12pt; "><span>Ricardo.</span></div><div style="font-size: 12pt; "> </div><div><font size="1" style="font-size: 12pt; "><i></i></font><font size="1" style="font-size: 12pt; "><i></i></font><div style="font-family: 'times new roman', 'new york', times, serif; "><style><!--filtered {font-family:"Cambria Math";panose-1:2 4 5 3 5 4 6 3 2 4;}filtered {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}p.MsoNormal, li.MsoNormal, div.MsoNormal
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style="font-size: 11px;"><br></span></div> <br></div></div><div style="font-size: 12pt; "><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; margin-top: 5px; padding-left: 5px;"> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <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> Ricardo O. S. Soares <ross_usp@yahoo.com.br>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Enviadas:</span></b> Quarta-feira, 2 de Maio de 2012 20:35<br> <b><span style="font-weight: bold;">Assunto:</span></b> Re: [gmx-users] NBFIX to gromacs<br> </font> </div> <br>The problem is that functype 1 for [
pairtypes ] when gromacs uses a CHARMM<br>forcefield is that gromacs treats them as 1-4 interactions. You will have to <br>ask/wait for someone familiar with the gromacs source to say if there is a <br>different functype available to use to override non-1-4 interactions with<br>the given pair parameters that you want to specify.<br><br><br>On 2012-05-02 12:35:17PM -0700, Ricardo O. S. Soares wrote:<br>> Dear Mr. Peter C. Lai,<br>> <br>> I appreciate your kind response.<br>> <br>> I apologize for the delay on my part.<br>> This NBFIX parameters that I'm working with came from the str file in <a href="http://terpconnect.umd.edu/~jbklauda/research/download/chol_new.str" target="_blank">http://terpconnect.umd.edu/~jbklauda/research/download/chol_new.str</a> , which dates from 2012.<br>> I successfully converted this whole file, now I'm wondering about this NBFIX section.<br>> 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?<br>> Thanks again,<br>> <br>> Ricardo.<br>> <br>> <br>> <br>> <br>> <br>> <br>> >________________________________<br>> > De: Peter C. Lai <<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>><br>> >Para: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> <br>> >Enviadas: Segunda-feira, 30 de Abril de 2012 20:46<br>> >Assunto: Re: [gmx-users] NBFIX to gromacs<br>> > <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 href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> >> Please don't post (un)subscribe requests to the list. Use the <br>> >> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> >> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>> ><br>> ><br>> >-- <br>> >==================================================================<br>> >Peter C.
Lai | University of Alabama-Birmingham<br>> >Programmer/Analyst | KAUL 752A<br>> >Genetics, Div. of Research | 705 South 20th Street<br>> ><a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>> >(205) 690-0808 |<br>> >==================================================================<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
href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> >Please don't post (un)subscribe requests to the list. Use the <br>> >www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> >Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>> ><br>> ><br>> ><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
href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br>-- <br>==================================================================<br>Peter C. Lai | University of Alabama-Birmingham<br>Programmer/Analyst | KAUL 752A<br>Genetics, Div. of Research | 705 South 20th Street<br><a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>
| Birmingham AL 35294-4461<br>(205) 690-0808 |<br>==================================================================<br><br><br><br> </div> </div> </blockquote></div> </div></body></html>