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>Vijayan.R<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 class="im"><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 class="im">> 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>
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<span class="HOEnZb"><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">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>
<a href="tel:%28205%29%20690-0808" value="+12056900808">(205) 690-0808</a> |<br>
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