<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><BR><DIV><DIV>On Oct 19, 2005, at 3:25 PM, Jim (Rui) Qiao wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Dear Gromacs users:<BR> <BR> I am trying to use the Cholesterol topology file uploaded by <FONT size="-1">Monika Hoeltje on the Gromacs server, and have a few questions: <BR> <BR> In the "cholesterol.itp" file, it writes:<BR> <BR> [ atoms ]<BR> ; nr type resnr residu atom cgnr charge ; total charge<BR> 1 CH3 1 CHOL C1 1 0<BR> 2 CB 1 CHOL C2 2 0<BR> ...<BR> ...<BR> [ bonds ]<BR> ; ai aj funct c0 c1<BR> 1 2 1 0.153 334720.<BR> 2 3 1 0.153 334720.<BR> 3 4 1<BR> 4 5 1<BR> 5 6 1<BR> ....<BR> ....<BR> <BR> It is noticed that the some parameters under [bonds] are not given. What does this mean? How will gromacs know where to look for these parameters?<BR></FONT> </BLOCKQUOTE></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>If you don't specify any explicit parameters grompp will pick up the default ones for these atomtypes from the forcefield.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Normally you only specify explicit parameters to override the default values.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>-----------------------------------------------------------</DIV><DIV>Erik Lindahl <<A href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</A>></DIV><DIV>Assistant Professor, Stockholm Bioinformatics Center</DIV><DIV>Stockholm University, SE 106 91 Stockholm</DIV><DIV>Phone: +46 8 5537 8564 Fax: +46 8 5537 8214</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></BODY></HTML>