<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><BR><BR>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>
<DIV id=yiv870674894>
<TABLE cellSpacing=0 cellPadding=0 border=0>
<TBODY>
<TR>
<TD vAlign=top>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'">Dear gmx-user,</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'"></SPAN> </DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'">I put <SPAN style="FONT-SIZE: 10pt; BACKGROUND: yellow; FONT-FAMILY: 'Arial', 'sans-serif'"><FONT style="BACKGROUND-COLOR: #ffff00"><FONT style="BACKGROUND-COLOR: #ffffff">#include "disre.itp"</FONT><SPAN><FONT style="BACKGROUND-COLOR: #ffffff"> at the end of</FONT><FONT style="BACKGROUND-COLOR: #ffffff"> </FONT></SPAN></FONT></SPAN><FONT style="BACKGROUND-COLOR: #ffffff">making</FONT> a hybrid [molecule] section as mark's suggestion, I got the same error after grompp. </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'">
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT style="BACKGROUND-COLOR: #ffff00"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"></SPAN></FONT>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT style="BACKGROUND-COLOR: #ffff00"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'">“<SPAN class=yshortcuts id=lw_1233041203_1 style="CURSOR: hand; BORDER-BOTTOM: #0066cc 1px dashed">Fatal error</SPAN>: [ file "../disre.itp", line 2 ]:</SPAN> </FONT>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"><FONT style="BACKGROUND-COLOR: #ffff00"><SPAN> </SPAN>Atom index (195) in distance_restraints out of bounds (1-1)”</FONT></SPAN> </DIV></DIV></SPAN>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'"></SPAN> </DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'">; <SPAN class=yshortcuts id=lw_1233041203_0 style="CURSOR: hand; BORDER-BOTTOM: #0066cc 1px dashed">File</SPAN> 'top.top' was generated; Include forcefield parameters<BR>;</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'">#include "/home/bio001/02_saow/gromacs_top/jit/top/ffgmx.itp"<BR>#include "/home/bio001/02_saow/gromacs_top/jit/popc.itp"</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'"><FONT style="BACKGROUND-COLOR: #ffffff">; Include chain topologies<BR></FONT><SPAN style="BACKGROUND: yellow"><FONT style="BACKGROUND-COLOR: #ffffff">#include "1add_H/0H_addH1.top"<SPAN> </SPAN>;protein atom 1-1615</FONT></SPAN></SPAN></DIV>
<DIV><FONT style="BACKGROUND-COLOR: #ff409f"><SPAN style="FONT-SIZE: 10pt; BACKGROUND: yellow; FONT-FAMILY: 'Arial', 'sans-serif'"><SPAN style="BACKGROUND: yellow"><FONT style="BACKGROUND-COLOR: #ffffff">#include "rimq1_top.itp"<SPAN> </SPAN>;ligand topology file 1-16</FONT></SPAN></SPAN></FONT></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'"><FONT style="BACKGROUND-COLOR: #ffffff">; Include water topology</FONT><BR>#include "/home/bio001/02_saow/gromacs_top/jit/top/flexspc.itp"</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'">#ifdef POSRES_WATER<BR>; Position restraint for each water oxygen<BR>[ position_restraints ]<BR>; i funct fcx fcy fcz<BR> 1 1 1000 1000 1000<BR>#endif</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'">; Include generic topology for ions<BR>#include "/home/bio001/02_saow/gromacs_top/jit/top/ions.itp"<BR>[ system ]<BR>; Name<BR>Protein</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'"><FONT style="BACKGROUND-COLOR: #ffff00">[ molecules ]</FONT><BR>; Compound #mols<BR><SPAN style="BACKGROUND: yellow">Protein_A 1<BR>RIM 4</SPAN><BR>POPC 74<BR>SOL 3763<BR>Cl 8</SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; BACKGROUND: yellow; FONT-FAMILY: 'Arial', 'sans-serif'"><FONT style="BACKGROUND-COLOR: #ffff00">#include "disre.itp"<SPAN> </SPAN></FONT></SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'">------------------------------------------</SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'">detailed in "disre.itp" file is<BR>[ distance_restraints ]</SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"> <SPAN> </SPAN>195<SPAN> </SPAN>1628<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>0.25 0.35 0.40 1.0</SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"><SPAN> </SPAN><SPAN> </SPAN>195<SPAN> </SPAN>563<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>0.25 0.35 0.40 1.0</SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"><SPAN> </SPAN><SPAN> </SPAN>598<SPAN> </SPAN>1644<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>0.25 0.35 0.40 1.0</SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"><SPAN> </SPAN><SPAN> </SPAN><SPAN> </SPAN>598<SPAN> </SPAN>966<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>0.25 0.35 0.40 1.0</SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"><SPAN> </SPAN><SPAN> </SPAN>1001<SPAN> </SPAN>1660<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>0.25 0.35 0.40 1.0</SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"><SPAN> </SPAN><SPAN> </SPAN>1001<SPAN> </SPAN>369<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>0.25 0.35 0.40 1.0</SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"><SPAN> </SPAN><SPAN> </SPAN>1404<SPAN> </SPAN>1676<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>0.25 0.35 0.40 1.0</SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"><SPAN> </SPAN><SPAN> </SPAN>1404<SPAN> </SPAN>160<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>1<SPAN> </SPAN>0.25 0.35 0.40 1.0</SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"><BR>I also try to merge the ligand into protein topology by using pdb2gmx but it can not file the forcefield for ligand. </SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial', 'sans-serif'"> </SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial', 'sans-serif'"><SPAN style="COLOR: #333333"><BR> Thanks so much<BR> <BR>pathum</SPAN></SPAN></DIV></TD></TR></TBODY></TABLE><BR></DIV></BLOCKQUOTE></td></tr></table><br>