Thank you for your informative reply, Sir, <br><br>Now I understood the problem but when i was tried with another ligand (GSSG) It could be simulated. Later I found error for different ligand.<br><br>please give me the solution, what sort of force field should be applied?<br>
<br><br><br><br><div class="gmail_quote">On 9 May 2011 21:27, ITHAYARAJA <span dir="ltr"><<a href="mailto:ithayaraja@gmail.com">ithayaraja@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Sir<br><br>Greetings!<br><br>I am following every gromacs
applications based on your manuals. I now get stuck in grompp -energy
minimization step during generation of .tpr file for my ligand and
protein. the error which i found is the following,<br>
<br><br>Ignoring obsolete mdp entry 'title'<br>Ignoring obsolete mdp entry 'cpp'<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#<br><br>WARNING 1 [file em.mdp, line unknown]:<br> Unknown or double left-hand 'coulomtype' in parameter file<br>
<br><br>checking input for internal consistency...<br>processing topology...<br>Opening library file /usr/share/gromacs/top/<div>ffG43a1.itp<br>Opening library file /usr/share/gromacs/top/ffG43a1nb.itp<br>Opening library file /usr/share/gromacs/top/ffG43a1bon.itp<br>
Opening library file /usr/share/gromacs/top/ff_dum.itp<br>Generated 279 of the 1225 non-bonded parameter combinations<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.7<br>Source code file: ../../../../src/kernel/toppush.c, line: 947<br>
<br>Fatal error:<br>Atomtype CB not found<br>-------------------------------------------------------<br><br>Sir,
I couldn't understand what did it refers to? So I kindly request you
spare your little time from your busy schedule to solve this problem.<br>
<br>Thank you, Sir<br></div><br clear="all"><br>-- <br><font color="#888888"><font size="2"><b></b></font><br>Ithayaraja M,<br>Research Scholar,<br>Department of Bionformatics,<br>Bharathiar University,<br>Coimbatore 641 046,<br>
Tamil Nadu<br>
India<br>
</font></blockquote></div><br><br clear="all"><br>-- <br><font size="2"><b></b></font><br>Ithayaraja M,<br>Research Scholar,<br>Department of Bionformatics,<br>Bharathiar University,<br>Coimbatore 641 046,<br>Tamil Nadu<br>
India<br>