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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The webserver is updated in May 2026 to support python3 and the new version pmx.
Generate hybrid structures/topologies for amino acid mutations
Structure file (.pdb):
...
Force field selection:
Amber99SB*ILDN
Amber14SB
Charmm36m
Number of mutations:
1
2
3
More
Perform a scan:
Select mutations:
1. Chain ID
(optional):
1. Amino acid
number:
1. Mutate to:
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, 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)
Use pdb2gmx to assign hydrogens?
email (optional):
Submit the query: