<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Chris,</div><div><br></div><div><blockquote type="cite"><font class="Apple-style-span" color="#000000"><br></font>I believe that the latest response had the wrong subject, so I am <br>changing it back.<br><br>Pär, two comments:<br>First, does that option really exist?<br><br>$ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z <br>2>&1; cat z|grep nochargegrp|wc -l<br><br></blockquote><div><div>The name flag is listed as [no]chargegrp</div><div><br></div></div><blockquote type="cite"><font class="Apple-style-span" color="#000000"><br></font>Second, I am not entirely convinced that one can discount the need for <br>gromacs-style charge groups. When CHARMM includes an atom in the <br>cutoff, it includes the entire charge group, but that doesn't mean the <br>algorithms of CHARMM and gromacs are entirely the same</blockquote><div>That's why I said if you know what you're doing :)</div><div><br></div><blockquote type="cite"><font class="Apple-style-span" color="#000000"><br></font>I gather that the large charge group listed below is the one that is <br>spurring the message:<br><br>GROUP ! H31<br>ATOM N NTL -0.60 ! |<br>ATOM C11 CTL2 -0.10 ! H33-C13-H32<br>ATOM C12 CTL5 -0.35 ! |<br>ATOM C13 CTL5 -0.35 ! H21 | H43<br>ATOM C14 CTL5 -0.35 ! | | |<br>ATOM H11 HL 0.25 ! H22-C12---N---C14-H42 (+)<br>ATOM H12 HL 0.25 ! | | |<br>ATOM H21 HL 0.25 ! H23 | H41<br>ATOM H22 HL 0.25 ! |<br>ATOM H23 HL 0.25 ! |<br>ATOM H31 HL 0.25 ! |<br>ATOM H32 HL 0.25 ! H11-C11-H12<br>ATOM H33 HL 0.25 ! |<br>ATOM H41 HL 0.25 ! |<br>ATOM H42 HL 0.25 ! |<br>ATOM H43 HL 0.25 ! |<br></blockquote>Yes, and probably one charge group in the arginine residue(s).</div><div><br></div><div>/Pär</div></body></html>