<br><br><div class="gmail_quote"><br><br><br>Dear Justin,<br><br>Thanks for the information.<br><br>Initially, i just wanted to run a simulation of protein-ligand in water solvent . I renamed the topology.top generated from mktop to ligand.itp; and included the ligand.itp line in the topol.top file generated from the pdb2gmx. During the pdb2gmx command, i used opls FF. The coordinates of ligand used as input for mktop were added to the output of pdb2gmx (process.pdb - only protein coordinates), so that the structure file along with ligand coordinates (processlig.pdb) can be used for further steps. I doubt whether the procedure followed by me is correct, as when i execute grompp command to add ions i am getting errors :<br>
<br><br>grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr<br><br>
<br>ERROR 1 [file ligand.itp, line 291]:<br> No default Ryckaert-Bell. types<br><br>..........<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.5.4<br>Source code file: toppush.c, line: 1526<br>
<br>Fatal error:<br>[ file ligand.itp, line 397 ]:<br>Atom index (0) in dihedrals out of bounds (1-53).<br>This probably means that you have inserted topology section "dihedrals"<br>in a part belonging to a different molecule than you intended to.<br>
In that case move the "dihedrals" section to the right molecule.<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br><br>The commands executed to reach the grompp step are as follows:<br><br><br>pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb<br>editconf -f processlig.pdb -o procent.pdb -princ<br>
editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic<br>genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top<br>grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr<br><br>I have attached the topol.top, ligand.itp files for your information, Please let me know your suggestions to fix this error.<br>
<br>Thanks,<br>Pramod<div><div></div><div class="h5"><br><br><br><br><br>
<div class="gmail_quote">On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><br>
<br>
ram bio wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs Users,<br>
<br>
I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is available for merging the output of mktop into gromacs MD simulation.<br>
<br>
<br>
</blockquote>
<br></div>
You can #include any molecule topology in a system .top, provided you have the right format:<br>
<br>
<a href="http://www.gromacs.org/Documentation/File_Formats/.itp_File" target="_blank">http://www.gromacs.org/<u></u>Documentation/File_Formats/.<u></u>itp_File</a><br>
<br>
There is no tutorial for using mktop with a protein-ligand/membrane system, but there are tutorials for protein-ligand complexes:<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin/<u></u>gmx-tutorials/complex/index.<u></u>html</a><br>
<br>
and membrane protein systems:<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin/<u></u>gmx-tutorials/membrane_<u></u>protein/index.html</a><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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