<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Thanks for the response. We will be using the CHARMM ff. </DIV>
<DIV><BR><BR>--- On <B>Thu, 5/5/11, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Justin A. Lemkul <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] RTP file formats<BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Thursday, May 5, 2011, 8:38 PM<BR><BR>
<DIV class=plainMail><BR><BR>Mr Bernard Ramos wrote:<BR>> Hi everyone!<BR>> The *.rtp file formats we have on Gromacs rtp file exmaples do not necessarily have the [dihedrals] or [impropers] part. They normally only have the [atoms] and [bonds]. In fact, the [bonds] section do not enumerate the constants or parameters. This is not what is written or <BR><BR>Different force fields work in different ways. Gromos, for instance, uses #define statements to replace listed gb_*, ga_*, etc.<BR><BR>> shown as an example in the manual. Is is ok to just enumerate or list <BR><BR>The manual shows a generic example, which may not be the same for all force fields.<BR><BR>> down the [atoms] and [bonds] but not including the rest? Thanks.<BR>> <BR><BR>Per the example in section 5.6.1, only the [bondedtypes] and [atoms] directives are mandatory, but in the case of a bonded molecule, I believe [bonds] are as well. The rest of the
directives, if not otherwise specified, are constructed from the existing information.<BR><BR>-Justin<BR><BR>-- ========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list <A href="http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="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"
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