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.
I attach the relevant files as well.
Best,
Batuhan
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- chemical/x-pdb attachment: 1.pdb
- text/plain attachment: leap
Received on Mon Sep 21 2015 - 03:30:05 PDT
