pmx: generate hybrid protein structure and topology
Computational Biomolecular Dynamics Group
aws benchmark
pmx protein web server
pmx DNA web server
Tripeptide DB
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Force field selection:
Amber99SB*ILDN
Amber14SB
Charmm36m
Select amino acids:
Amino acid #1:
Amino acid #2
A (alanine)
R (arginine)
N (asparagine)
D (aspartate)
B (aspartate protonated)
C (cysteine)
G (glycine)
E (glutamate)
J (glutamate protonated)
Q (glutamine)
X (histidine: only Nε2 protonated)
H (histidine: only Nδ1 protonated)
Z (histidine: Nε2 and Nδ1 protonated)
I (isoleucine)
L (leucine)
K (lysine)
O (lysine unprotonated)
M (methionine)
F (phenylalanine)
S (serine)
T (threonine)
W (tryptophan)
Y (tyrosine)
V (valine)
A (alanine)
R (arginine)
N (asparagine)
D (aspartate)
B (aspartate protonated)
C (cysteine)
G (glycine)
E (glutamate)
J (glutamate protonated)
Q (glutamine)
X (histidine: only Nε2 protonated)
H (histidine: only Nδ1 protonated)
Z (histidine: Nε2 and Nδ1 protonated)
I (isoleucine)
L (leucine)
K (lysine)
O (lysine unprotonated)
M (methionine)
F (phenylalanine)
S (serine)
T (threonine)
W (tryptophan)
Y (tyrosine)
V (valine)