Re: [gmx-users] constraints between protein ligand - metal chelation

This approach still requires the system to be parameterized as a single moleculetype, doesn't it? On 2012-05-20 04:42:26PM +0200, francesco oteri wrote: Hi, if you are able to define atom couples able to mantein the structure of your complex, you can insert in .top file a set of bond using

Re: [gmx-users] constraints between protein ligand - metal chelation

You are right Peter 2012/5/21 Peter C. Lai p...@uab.edu This approach still requires the system to be parameterized as a single moleculetype, doesn't it? On 2012-05-20 04:42:26PM +0200, francesco oteri wrote: Hi, if you are able to define atom couples able to mantein the structure of

Re: [gmx-users] constraints between protein ligand - metal chelation

Many thanks for your response On Mon, May 21, 2012 at 12:01 PM, francesco oteri francesco.ot...@gmail.com wrote: You are right Peter 2012/5/21 Peter C. Lai p...@uab.edu This approach still requires the system to be parameterized as a single moleculetype, doesn't it? On 2012-05-20

Re: [gmx-users] constraints between protein ligand - metal chelation

Hi, if you are able to define atom couples able to mantein the structure of your complex, you can insert in .top file a set of bond using function 6 (see table at pag 125 of the user manual). For example, let atom 1 and 100 are at distance 0.6nm, you can insert in .top a row like 1 100 6 0.6 1000

[gmx-users] constraints between protein ligand - metal chelation

Dear Gromacs users I was wondering if there exists any technique that sets distance restraint between specified ligand (atoms) and the protein(atoms) in Gromacs. I am simulating a system which contains metal ions coordinated to the Ligand. I looked in to the mailing list and Gromacs manual and

Re: [gmx-users] constraints between protein ligand - metal chelation

Is there a particular reason why the ligand has been parameterized as a separate moleculetype from the protein in your case? I prefer to treat coordination bonds as real bonds instead of relying on electrostatic interactions anyway, since it is the only way to conservatively ensure the

Re: [gmx-users] constraints between protein ligand - metal chelation

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. Regards Vijayan.R On Sat,