Hello, from my own expierence I can say that
atomic charges calculated with Gaussian are good charges.
2015-09-17 1:37 GMT-03:00 Pallavi Banerjee <
pallavis...@students.iiserpune.ac.in>:
> Thanks Justin. Things are clearer now.
>
> -Pallavi Banerjee
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> Gromacs Users mailing list
>
> * Please
Thanks Justin. Things are clearer now.
-Pallavi Banerjee
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On 9/16/15 12:27 AM, Pallavi Banerjee wrote:
Hello users,
I have this confusion regarding the atomic charges that gromacs sees. I
have defined my residues in aminoacids.rtp file with my own charges, but
the atom types for the same in the ffnonbonded.itp have different charges
on them. Which of
The forcefield is OPLS-AA. I put in the modified charges for the residue in
the aminoacids.rtp file. The topology generated also shows the same charges
that I put. But I was wondering if the charges defined for the atomtypes in
the ffnonbonded.itp overrride these.
Thanks and regards,
-Pallavi Ban
Which force field are you using? How did you obtain the charges? OPLSAA has
its own charges., which can be modified for new molecules.
Chandan
On Wed, Sep 16, 2015 at 9:57 AM, Pallavi Banerjee <
pallavis...@students.iiserpune.ac.in> wrote:
> Hello users,
>
> I have this confusion regarding the a
Hello users,
I have this confusion regarding the atomic charges that gromacs sees. I
have defined my residues in aminoacids.rtp file with my own charges, but
the atom types for the same in the ffnonbonded.itp have different charges
on them. Which of the two charges would Gromacs pick?
Thank you.
Dear Oliver, I’d recommend to try http://q4md-forcefieldtools.org/REDS/. If
you did all right, it should t least confirm your RESP results.
Alan
On 19 May 2014 07:20, Oliver Schillinger wrote:
> Hi everyone,
>
> I am trying to parametrize a ligand for use with the amber force fields
> (amber99
Hi everyone,
I am trying to parametrize a ligand for use with the amber force fields
(amber99sb-nmr1 in particular:
https://research.chemistry.ohio-state.edu/bruschweiler/protein-force-field/).
The ligand is EGCG (http://en.wikipedia.org/wiki/Epigallocatechin_gallate).
The main focus of our s
