Dear Justin,
Thank you for your reply. I have parameters from some manuscript and add
all of them in force field. There is two parts of dihedral types in
ffbonded.itp that one of them has func=4 and another has func=9. Also I
have two types of parameters for dihedral;* Proper* and* Improper
On 2/11/16 12:03 PM, Malihe Hasanzadeh wrote:
Hi
I have three water molecules and one new residue that I want to add their
parameters to force field Amber99sb. One of water molecules has only one
hydrogen, and since I want to prevent from replacing with SOL in solvation
step, So I define them
Hi
I have three water molecules and one new residue that I want to add their
parameters to force field Amber99sb. One of water molecules has only one
hydrogen, and since I want to prevent from replacing with SOL in solvation
step, So I define them as new residue in .rtp file:
[ INN ]
[ atoms ]
Hi
I want to add some bond parameters in ffbonded.itp file, and
as I read in manual, unit of "kb" is "kj.mol-1.nm-2" and
unit of "b0" is "nm". But I have these quantities with
"kcal.mol-1.Å-2" and "Å". How do I convert these? Is it
enough converting of kcal/mol to kj/mol for "kb" and "Å" to
On 2/9/16 5:04 PM, Mahnaz Mirsoltani wrote:
Hi
I want to add some bond parameters in ffbonded.itp file, and
as I read in manual, unit of "kb" is "kj.mol-1.nm-2" and
unit of "b0" is "nm". But I have these quantities with
"kcal.mol-1.Å-2" and "Å". How do I convert these? Is it
Unit
