<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I believe that there's no problem with the numbering. The numbering in the topology will start with 1, however due to Gromacs' implementation, the indexing starts at 0. So, atom 4036 in your .itp corresponds to 4035 in the trajectory file. Note that if you look in your trajectory file you should see an atom indexed at 0. For example:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> x[ 0]={ 9.82700e+00, 6.47400e+00, 1.01800e+01}</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">hth</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Jim</DIV><BR><DIV><DIV>On Mar 3, 2006, at 10:00 AM, Michal Kolinski wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> <DIV><FONT face="Arial" size="2">Dear All</FONT></DIV> <DIV> </DIV> <DIV><FONT face="Arial" size="2">I’m using distance restraints to force proper orientation of the ligand in the active site of the receptor protein (I’m investigating different binding modes).<BR>I encountered a strange problem when defining distance restraints.<BR>I have protein and ligand topology combined in one itp file.<BR>At the end of this topology file (itp) I defined atoms pairs for distance restraints:<BR>….<BR>[ distance_restraints ]<BR>; ai aj type index type low up1 up2 fac<BR> 1384 4036 1 0 1 0.0 0.15 0.25 2.0<BR> 2957 4046 1 1 1 0.0 0.15 0.25 2.0<BR> 2957 4057 1 1 1 0.0 0.15 0.25 2.0</FONT></DIV> <DIV> </DIV> <DIV><FONT face="Arial" size="2">When looking at trajectory file I noticed that restraints are present but not between defined atoms but probably between pairs:</FONT></DIV> <DIV> </DIV> <DIV><FONT face="Arial" size="2">1383 4035<BR>2956 4045<BR>2956 4056</FONT></DIV> <DIV> </DIV> <DIV><FONT face="Arial" size="2">I checked the tpr file: gmxdump_mpi3 -s posre100.tpr and I found that position restraints are not between defined pairs but rather between (atom-1,atom-1).<BR>…<BR>Dis. Rest.:<BR> nr: 9<BR> multinr[division over processors]: 9 9 9 9 9 9 9 9 9 9 9 9 …<BR> iatoms:<BR> 0 type=1244 (DISRES) 1383 4035<BR> 1 type=1245 (DISRES) 2956 4045<BR> 2 type=1245 (DISRES) 2956 4056<BR>…</FONT></DIV> <DIV> </DIV> <DIV><FONT face="Arial" size="2">Numbering of atoms in my topology file is correct so I guess it’s not the case. What might be the problem. Am I doing something wrong. I’m using gromacs3.3. Please give me comment on this and thank you for help.<BR></FONT></DIV> <DIV><FONT face="Arial" size="2"></FONT> </DIV> <DIV><FONT face="Arial" size="2">Best regards<BR>Michal<BR></FONT></DIV><FONT face="Arial" size="2"></FONT><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; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR></BODY></HTML>