<div>Hi Mark,</div> <div>I'm so sorry for taking so much of your time.I tried to explain how I generated the sections:</div> <div> </div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman">Firstly I<SPAN style="mso-spacerun: yes"> </SPAN>named my ligand (protein) files as<SPAN style="mso-spacerun: yes"> </SPAN><B style="mso-bidi-font-weight: normal">drg</B><SPAN style="mso-spacerun: yes"> </SPAN>and my protein<SPAN style="mso-spacerun: yes"> </SPAN>files as <B style="mso-bidi-font-weight: normal">trp.<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></B></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>Next I generated the drg.itp and trp.top <SPAN style="mso-spacerun: yes"> </SPAN>files
with pdb2gmx</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>pdb2gmx <SPAN style="mso-spacerun: yes"> </SPAN>-ff gmx -f drg.pdb -o drg2 -p drg.top</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>pdb2gmx <SPAN style="mso-spacerun: yes"> </SPAN>-ff gmx -f trp.pdb -o trp2.pdb<SPAN style="mso-spacerun: yes"> </SPAN>-p trp.top<SPAN style="mso-spacerun: yes"> </SPAN>-merge -ignh –ss</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>Then I pasted the coordinates from drg.pdb onto the end of the trp2.file and I edited trp.top file; I added <SPAN style="mso-spacerun:
yes"> </SPAN>#include “ drg.itp” and under the [molecules] section my ligand.</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>I setup the box.</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>editconf -bt octahedron -f trp2.pdb -o trp2.pdb -c -d 0.8</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman">genbox -cp trp2.pdb<SPAN style="mso-spacerun: yes"> </SPAN>-cs spc216.gro -o trp_b4ion.pdb -p trp.top<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div>
<div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><U><FONT size=3><FONT face="Times New Roman"><STRONG>My em.mdp file <o:p></o:p></STRONG></FONT></FONT></U></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>title = drg_trp</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>cpp = /usr/bin/cpp</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>define = -DFLEX_SPC</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT
face="Times New Roman" size=3>constraints = none</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>integrator = steep</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>dt = 0.002</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>nsteps = 500</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>nstlist = 10</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>ns_type = grid</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>rlist = 0.9</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>coulombtype = cutoff</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>rcoulomb = 0.9</FONT></div> <div
class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>rvdw = 0.9</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>fourierspacing = 0.12</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>fourier_nx = 0</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>fourier_ny = 0</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>fourier_nz = 0</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>pme_order = 4</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>ewald_rtol = 1e-5</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>optimize_fft = yes</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New
Roman" size=3>emtol = 1000.0</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman">emstep = 0.01<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>grompp -f em.mdp -c trp_b.pdb -p trp.top -o trp_b.tpr</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>After grompp ý got these error.</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>ERROR 1 [file "drg.itp", line 7]:</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm
0pt; TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>ERROR 2 [file "drg.itp", line 8]:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>ERROR 3 [file "drg.itp", line 9]:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</FONT></FONT></div> <div
class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>ERROR 4 [file "drg.itp", line 10]:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>ERROR 5 [file "drg.itp", line 11]:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>ERROR 6 [file "drg.itp", line 12]:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt;
TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>ERROR 7 [file "drg.itp", line 13]:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>ERROR 8 [file "drg.itp", line 14]:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</FONT></FONT></div> <div
class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>ERROR 9 [file "drg.itp", line 15]:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>ERROR 10 [file "drg.itp", line 16]:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>Cleaning up temporary file gromppWX2Ly6</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt;
TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>-------------------------------------------------------</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>Program grompp_mpi, VERSION 3.3.1</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>Source code file: fatal.c, line: 416</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>Fatal error:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman" size=3>Too many warnings, grompp_mpi terminated</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 6pt"><FONT face="Times New Roman"
size=3>-------------------------------------------------------</FONT></div> <div>Fulya<BR><BR><B><I>Mark Abraham <Mark.Abraham@anu.edu.au></I></B> wrote:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">fulya caglar wrote:<BR>> Hi Mark,<BR>> I checked my .top file and I saw that there is no q0 column under the <BR>> [dihedrals] in the complex topology file but there is q0 column in the <BR>> ligand protein .top file.Dou you think that it is the source of my <BR>> problem?Thanks very much.<BR><BR>I don't know... you'll have to give examples and explain *fully* how you <BR>generated the sections.<BR><BR>Mark<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use
the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> 
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