<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi,<DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On Oct 16, 2005, at 6:34 PM, Lei Zhou wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV>Hi, </DIV> <DIV>thanks for the reply. I have removed those two 0's from the "imp" part and now the grompp (of 3.3) is working. The modified ligand.itp is looks like this:</DIV> <DIV><FONT face="courier new,monospace" size="1">3 1 4 13 2 35.3 334.8 35.3 334.8 ; imp C2* O2* C3* C1*</FONT></DIV> <DIV><FONT face="courier new,monospace" size="1">4 3 5 11 2 35.3 334.8 35.3 334.8 ; imp C3* C2* O3* C4*</FONT></DIV> <DIV><FONT face="courier new,monospace" size="1">....</FONT></DIV> <DIV><FONT face="courier new,monospace" size="1">13 3 1 2 1 0.0 1.3 3 0.0 1.3 3 ; dih C1* C2* O2* H8L</FONT></DIV> <DIV><FONT face="courier new,monospace" size="1">11 4 3 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C4* C3* C2* O2*</FONT></DIV> <DIV><FONT face="courier new,monospace" size="1">....</FONT></DIV> <DIV>I didn't do anything to the "dih" part. Is this correct, with two extra columns representing "multi" for "dih" (3's shown above)? </DIV> <DIV> </DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV>That looks correct.</DIV><DIV><BR><BLOCKQUOTE type="cite"> <DIV>Another question is related with this. For the old grompp of 3.2.1, it didn't give any warning about the extra "0"s for the impropers. Does this affect the original MD results by 3.2.1?</DIV></BLOCKQUOTE><BR></DIV><DIV>No, unless you were doing free energy runs - then it might have had an effect, but even in that case it's easy to check - just rerun a couple of steps with the new topology and check for differences.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</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></DIV></BODY></HTML>