On Mon, Sep 21, 2015 at 6:23 AM, Batuhan Kav <bkav13.ku.edu.tr> wrote:
> Dear All,
>
> I am trying to set up a simple carbohydrate simulation in Amber. I
> observe some differences between leap and glycam-web generated parameter
> files. I would like to ask what might be the reason for such difference.
>
> So, here are the details. I created a pdb file in glycam-web builder.
> Then, glycam-web gives me 1_Amber.pdb, which I think is ready to be used
> in leap. Glycam-web also gives me 1.parm7 file.
>
> I delete connectivity from 1_Amber.pdb, and load it into leap using
> Glycam-06 parameters. Then, I create the amber parameter files using
> saveAmberparm.
>
> When I compare two parameter files, I observe some differences. For
> instance, in some flags like BOND_FORCE_CONSTANT and ANGLE_EQUIL_VALUE,
> the number of entries are different for each file. So I wonder what
> might I be doing wrong here? I was expecting to obtain nearly identical
> files with the both procedures.
>
Two prmtops can give identical energies and forces but still be very
different if you simply compare their contents. The best way to really
compare two prmtops is to calculate the energy with the same set of
coordinates for both topology files and make sure it comes out identical.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 21 2015 - 04:30:03 PDT
