<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'">Dear gmx-users,<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"> <o:p></o:p></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'">Do you know how to make distance restraint between ligand and protein in gromacs?<BR>I have a chain of protein binds with 4 </SPAN><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'; mso-bidi-font-family: Tahoma">drugs in water-lipid box, the topology put below..</SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"><BR style="mso-special-character: line-break"><BR style="mso-special-character: line-break"><o:p></o:p></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'">; File 'top.top' was generated; Include forcefield parameters<BR>;<o:p></o:p></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"<o:p></o:p></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'">; Include chain topologies<BR><SPAN style="BACKGROUND: yellow; mso-highlight: yellow">#include "1add_H/0H_addH1.top"<SPAN style="mso-spacerun: yes"> </SPAN>;protein atom 1-1615<o:p></o:p></SPAN></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; BACKGROUND: yellow; FONT-FAMILY: 'Arial','sans-serif'; mso-highlight: yellow">#include "disre.itp"<SPAN style="mso-spacerun: yes"> </SPAN>; distance restraint topology file<o:p></o:p></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; BACKGROUND: yellow; FONT-FAMILY: 'Arial','sans-serif'; mso-highlight: yellow">#include "rimq1_top.itp"<SPAN style="mso-spacerun: yes"> </SPAN>;ligand topology file atom 1-16</SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"><o:p></o:p></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'">; Include water topology<BR>#include "/home/bio001/02_saow/gromacs_top/jit/top/flexspc.itp"<o:p></o:p></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<o:p></o:p></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<o:p></o:p></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'">[ molecules ]<BR>; Compound #mols<BR><SPAN style="BACKGROUND: yellow; mso-highlight: yellow">Protein_A 1<BR>RIM 4</SPAN><BR>POPC 74<BR>SOL 3763<BR>Cl 8<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><o:p> </o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'">------------------------------------------<o:p></o:p></SPAN></DIV>
<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 ]<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"> <SPAN style="mso-spacerun: yes"> </SPAN>195<SPAN style="mso-spacerun: yes"> </SPAN>1628<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.25 0.35 0.40 1.0<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>195<SPAN style="mso-spacerun: yes"> </SPAN>563<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.25 0.35 0.40 1.0<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>598<SPAN style="mso-spacerun: yes"> </SPAN>1644<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.25 0.35 0.40 1.0<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>598<SPAN style="mso-spacerun: yes"> </SPAN>966<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.25 0.35 0.40 1.0<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>1001<SPAN style="mso-spacerun: yes"> </SPAN>1660<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.25 0.35 0.40 1.0<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>1001<SPAN style="mso-spacerun: yes"> </SPAN>369<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.25 0.35 0.40 1.0<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>1404<SPAN style="mso-spacerun: yes"> </SPAN>1676<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.25 0.35 0.40 1.0<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>1404<SPAN style="mso-spacerun: yes"> </SPAN>160<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.25 0.35 0.40 1.0<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><BR>The error occur after grompp run is..<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><o:p> </o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'">“Fatal error: [ file "../disre.itp", line 2 ]:<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><SPAN style="mso-spacerun: yes"> </SPAN>Atom index (1628) in distance_restraints out of bounds (1-1615)”<o:p></o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'"><o:p> </o:p></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'">It seems to be that the atoms from ligand (</SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'">rimq1_top.itp<SPAN style="COLOR: #333333">) topology was not known.<BR style="mso-special-character: line-break"><BR style="mso-special-character: line-break"><o:p></o:p></SPAN></SPAN></DIV>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: #333333; FONT-FAMILY: 'Arial','sans-serif'">My question is <BR>Q1: Where I should put “disre.itp” in topology file that it can recognize the atom from both protein (</SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'">0H_addH1.top<SPAN style="COLOR: #333333">) and ligand (</SPAN>rimq1_top.itp<SPAN style="COLOR: #333333">) topology files. <BR><BR> Thanks so much<BR> <BR>pathum</SPAN></SPAN></DIV></td></tr></table><br>