Dear Justin,<br><br>As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during md simulations in lipid bi layer. I found that MKTOP can generate topology files using opls ff for small molecules.<br>
<br> I have also tried swiss param to generate the ligand parameters to be used in protein
ligand simulation using gromacs. The force field i am using for
simulations is OPLS. My ligand contains an azido group and a tropane
ring with protonated nitrogen. SwissParam force field has been designed to be compatible with the Charmm force field, but they are not tested on opls.Using the ligand topologies from swissparam, i was able to run the MD simulations using gromacs with opls without errors (swissparam - gromacs tutorial), only issues being the charges on the ligand, so i generated various input files (mol2 files) for swissparam with charges generated using ambcc1, gastergier and MMFF. But the itp files obtained from swissparam had same charges for the ligand atoms irrespective of the input provided i.e. charged or uncharged mol2 files, and<br>
<br>As per Gromacs website:<br><br> "Note that an <a title="Documentation/File_Formats/.itp_File" rel="internal" href="http://www.gromacs.org/Documentation/File_Formats/.itp_File">.itp file</a> will be specific to a given force field, and will only function when included by a <a title="Documentation/File_formats/.top_File" rel="internal" href="http://www.gromacs.org/Documentation/File_Formats/.top_File">.top file</a> that has previously included the <a title="Documentation/File_Formats/.itp_File" rel="internal" href="http://www.gromacs.org/Documentation/File_Formats/.itp_File">.itp files</a> for that force field. Appropriate use of the <code>#define</code> and <code>#ifdef</code> mechanisms can permit the same <a title="Documentation/File_Formats/.itp_File" rel="internal" href="http://www.gromacs.org/Documentation/File_Formats/.itp_File">.itp file</a> to work with multiple force fields, e.g. <code>share/top/water.itp</code>."<br>
<br>so, i think even though the swissparam generated topologies based on MMFF fit to charmm (based on testing), they could also be used with opls. It was informed by swiss param team that the ligand parameters generated by swissparam
could also be used with opls FF in principle as they are based on MMFF<br>So, in order to cross check or validate my results i was trying to use mktop to generate the ligand topologies for MD simulations.<br><br>Please let me know your comments and suggestions on the procedure , regarding the compatibility of MMFF generated topologies to be used by OPLS and other methods to validate my results.<br>
<br>Thanks,<br><br>Pramod<br><br><div class="gmail_quote">On Wed, Oct 12, 2011 at 1:28 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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><div></div><div class="h5"><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 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>
------------------------------<u></u>-------------------------<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/<u></u>Documentation/Errors</a><br>
------------------------------<u></u>-------------------------<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 and procentsolv.gro files for your information, Please let me know your suggestions to fix this error.<br>
<br>
</blockquote>
<br></div></div>
The ligand.itp file is trash. Most of your atoms have zero charge (except for a few that have +/- 1...yikes!) and on line 397 (as cited in the error message) atom 0 is referenced, which of course does not exist, since numbering starts with 1. You also have some exotic atom types present, and thus bonded parameters cannot be assigned, as grompp complained earlier.<br>
<br>
You need a better quality topology, and perhaps a different force field that might be suited for doing these simulations.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks,<br>
Pramod<div class="im"><br>
<br>
<br>
<br>
<br>
On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
ram bio wrote:<br>
<br>
Dear Gromacs Users,<br>
<br>
I am using opls FF for my protein-ligand simulations in lipid<br>
bilayer. I have generated the topologies for the ligand using<br>
MKtop. The output from the MKTOP gives the top file, but not the<br>
coordinate/structure file. Please let me know if any tutorial is<br>
available for merging the output of mktop into gromacs MD<br>
simulation.<br>
<br>
<br>
<br>
You can #include any molecule topology in a system .top, provided<br>
you have the right format:<br>
<br></div>
<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><div class="im"><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<br>
system, but there are tutorials for protein-ligand complexes:<br>
<br></div>
<a href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>__<a href="http://vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html" target="_blank"><u></u>vt.edu/Pages/Personal/justin/_<u></u>_gmx-tutorials/complex/index._<u></u>_html</a><div class="im">
<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></div>
<a href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>__<a href="http://vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html" target="_blank"><u></u>vt.edu/Pages/Personal/justin/_<u></u>_gmx-tutorials/membrane___<u></u>protein/index.html</a><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>
-- ==============================<u></u>__==========<div class="im"><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></div>
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==============================<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>
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