Hi,<div>if you are able to define atom couples able to mantein the structure of your complex,</div><div>you can insert in .top file a set of bond using function 6 (see table at pag 125 of the user manual). </div><div>For example, let atom 1 and 100 are at distance 0.6nm, you can insert in .top a row like</div>
<div><br></div><div>1 100 6 0.6 1000</div><div><br></div><div>you impose a bond between the two atoms having as eauilibrium distance 0.6nm and </div><div>force strenght 1000J.</div><div><br></div><div>Function 6 doesn't implie the generation of angles and dihedrals so it is the right choice </div>
<div>to impose distance restraints</div><div><br></div><div><br></div><div>Francesco<br><div class="gmail_quote">2012/5/20 R.S.K.Vijayan <span dir="ltr"><<a href="mailto:biovijayan@gmail.com" target="_blank">biovijayan@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Many thanks for your response. No special reasons for parametrizing the ligand and the protein as a separate system. I dont think that the ligand and protein can be parametrized as a single system, but will definitely try doing it as a single system and see if it works.<div>
Regards</div><div><span class="HOEnZb"><font color="#888888">Vijayan.R</font></span><div><div class="h5"><br><br><div class="gmail_quote">On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Is there a particular reason why the ligand has been parameterized as a<br>
separate moleculetype from the protein in your case? I prefer to treat<br>
coordination bonds as "real bonds" instead of relying on electrostatic<br>
interactions anyway, since it is the only way to conservatively ensure the<br>
coordination geometry is preserved (like for Zn, where QM predicts a<br>
tetrahedral geometry but Zn free ions will result in an octahedral geometry).<br>
In any case, even if you stick with freeion Zn, you can paramaterize the<br>
complex as a single moleculetype and use distance restraints there, can't<br>
you?<br>
<div><br>
<br>
On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote:<br>
> Dear Gromacs users<br>
><br>
> I was wondering if there exists any technique that sets<br>
> distance restraint between specified ligand (atoms) and the protein(atoms)<br>
> in Gromacs. I am simulating a system which contains metal ions coordinated<br>
> to the Ligand. I looked in to the mailing list and Gromacs manual and<br>
</div>> figured out that *genrster* can be employed, to<br>
<div>> set distance, position and dihedral restraints. Unfortunately i also<br>
> stumbled on the fact that restraints between systems is not possible.<br>
><br>
> Since force fields are not good at handling chelation between metal atoms,<br>
> i find that the metals drifting away from the coordinated ligand atoms<br>
> during the course of simulation, hence i introduced position constraints<br>
> for the metal and ended up realizing that the coordination distance<br>
> between the ligand and the metal exceeds the permissible range and the<br>
> angles between the chelating atoms gets distorted and some coordinating<br>
> residues like Histidine and Aspartic acid also moves away from the metal.<br>
><br>
> Hence, i was wondering if l anyone knows of any method (apart from<br>
> QM/MM) that can help to set distance restraints between the protein (metal<br>
> ion ) and the ligand, also any suggestion that could help in handling<br>
> ligand metal chelation is welcomed.<br>
> Thanking in advance<br>
><br>
><br>
> Regards<br>
><br>
> Vijayan.R<br>
<br>
</div>> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<span><font color="#888888"><br>
<br>
--<br>
==================================================================<br>
Peter C. Lai | University of Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>
<a href="tel:%28205%29%20690-0808" value="+12056900808" target="_blank">(205) 690-0808</a> |<br>
==================================================================<br>
<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></span></blockquote></div><br></div></div></div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco<br>
</div>