Many thanks for your response<br><br><div class="gmail_quote">On Mon, May 21, 2012 at 12:01 PM, francesco oteri <span dir="ltr"><<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">You are right Peter<br><br><div class="gmail_quote">2012/5/21 Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>></span><div>
<div class="h5"><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
This approach still requires the system to be parameterized as a single<br>
moleculetype, doesn't it?<br>
<div><div><br>
On 2012-05-20 04:42:26PM +0200, francesco oteri wrote:<br>
> Hi,<br>
> if you are able to define atom couples able to mantein the structure of<br>
> your complex,<br>
> you can insert in .top file a set of bond using function 6 (see table at<br>
> pag 125 of the user manual).<br>
> For example, let atom 1 and 100 are at distance 0.6nm, you can insert in<br>
> .top a row like<br>
><br>
> 1 100 6 0.6 1000<br>
><br>
> you impose a bond between the two atoms having as eauilibrium distance<br>
> 0.6nm and<br>
> force strenght 1000J.<br>
><br>
> Function 6 doesn't implie the generation of angles and dihedrals so it is<br>
> the right choice<br>
> to impose distance restraints<br>
><br>
><br>
> Francesco<br>
> 2012/5/20 R.S.K.Vijayan <<a href="mailto:biovijayan@gmail.com" target="_blank">biovijayan@gmail.com</a>><br>
><br>
> > Many thanks for your response. No special reasons for parametrizing the<br>
> > ligand and the protein as a separate system. I dont think that the ligand<br>
> > and protein can be parametrized as a single system, but will definitely try<br>
> > doing it as a single system and see if it works.<br>
> > Regards<br>
> > Vijayan.R<br>
> ><br>
> ><br>
> > On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai <<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>> wrote:<br>
> ><br>
> >> 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<br>
> >> 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>
> >><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<br>
> >> protein(atoms)<br>
> >> > in Gromacs. I am simulating a system which contains metal ions<br>
> >> coordinated<br>
> >> > to the Ligand. I looked in to the mailing list and Gromacs manual and<br>
> >> > figured out that *genrster* can be employed, to<br>
> >> > 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<br>
> >> 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<br>
> >> 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<br>
> >> (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>
> >> > --<br>
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> >><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>
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> >><br>
> >> --<br>
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> ><br>
> > --<br>
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><br>
><br>
><br>
> --<br>
> Cordiali saluti, Dr.Oteri Francesco<br>
<br>
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<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>
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</div></div></blockquote></div></div></div><div class="HOEnZb"><div class="h5"><br><br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco<br>
</div></div><br>--<br>
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