Dear AMBER users
I run simulations of protein-membrane complexes and now I tried to
visualize trajectories. I prepared the input files using CHARMM-GUI and
also used the topology files that I got from the web-server for
simulations. My system contains DOPS for which the force field (lipid 14)
for this lipid is not yet available in AMBER16. Therefore, I use charmm36
force field from CHARMM-GUI for my simulations. When I load the parm file
that I got from CHARMM-GUI in vmd, I got this messages
Info) Atoms: 315920
Info) Bonds: 0
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 315920
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 315920 Protein: 0 Nucleic: 0
It seems that there is no information about bonding between atoms therefore
when I load trajectories file I can’t visualize structure properly (atoms
represent at dot and are not connected to each other to form structure). I
check the parm file but there are also the sections such as
%FLAG BONDS_INC_HYDROGEN
%FLAG BONDS_WITHOUT_HYDROGEN
which should give information about bonding.
I would like to know how to change/modify or give bond information in the
parm file in order to visualize structure and trajectories properly and
nicely.
Best Regards,
Kanin Wichapong
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Received on Wed Sep 20 2017 - 09:30:01 PDT
