<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div><span class="Apple-style-span" style="font-family: times, serif; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> I was trying to calculate the <span class="yshortcuts" id="lw_1303345020_0">dipole moment</span> of part of my peptide. In other words, if I have a 10-residue peptide, I was interested in calculating the dipole-moment contribution of the backbone. So, I made an index file which have a group containing backbone atoms. But, if I try to use g_dipoles to get the dipole moment contribution from the backbone atoms, using following command:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left:
0px; ">g_dipoles -s -f traj -n index.ndx</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I get an error :</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Program g_dipoles_mod_4mpi, VERSION 4.0.5</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Source code file: gmx_dipoles.c, line: 1173</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="yshortcuts" id="lw_1303345020_1">Fatal error</span>:</div><div style="margin-top:
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">index[1]=197 does not correspond to the first atom of a molecule</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-------------------------------------------------------</div></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Any help how to get around this will be appreciated.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sanku</div></span></div><div style="position:fixed"></div>
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