Re: [gmx-users] charge calculation........

As mentioned, you should make RESP charges for AMBER parameters. ESP parameters are furthermore often a bit bizarre (aliphatic carbons with charge well below -1etc.). Erik 14.11 skrev tarak karmakar: > Thanks Mark. > > I have gone through the link "Parameterization of novel molecules" and > I

Re: [gmx-users] charge calculation........

Thanks Mark. I have gone through the link "Parameterization of novel molecules" and I see quantum calculations can be handy for this type of charge calculation (AMBER). So for the unprotonated tyrosine, I am taking two more amino acids (left and right) and calculating ESP charges of the tri-peptid

[gmx-users] charge calculation........

Hi Since you want to use the AMBER force for your calculations, you will need to compute the RESP charges for your new residue (unprotoned TYR) and add the charges in your *rtp file. To compute the charges, you can use the RED.Server (http://q4md-forcefieldtools.org/REDS/). It is not easy, s

Re: [gmx-users] charge calculation........

On 17/09/2012 10:01 PM, tarak karmakar wrote: Dear All, I want to have one of tyrosine residues in my protein to be unprotonated. I am using amber force field for the simulation. But in aminoacid.rtp there is no entry for the unprotonated one. So I am adding it by myself in to the

[gmx-users] charge calculation........

Dear All, I want to have one of tyrosine residues in my protein to be unprotonated. I am using amber force field for the simulation. But in aminoacid.rtp there is no entry for the unprotonated one. So I am adding it by myself in to the .rtp file. Now I am bit confused with the charge

Re: [gmx-users] Charge calculation in Gromacs

> Dear All who may concern, > I have some questions for the charge calculation in Gromacs, I used > the > forcefied ffG43a1 for the protein and inhibitors. Does the charge for the > protein is the charge per residue? The charge on a residue is the sum of the charges on the (united) atoms that

[gmx-users] Charge calculation in Gromacs

Dear All who may concern,    I have some questions for the charge calculation in Gromacs, I used the forcefied ffG43a1 for the protein and inhibitors. Does the charge for the protein is the charge  per residue? This forcefield is just for the polar H, right? For the nonpolar H, it will merge the H