From: Liqun Zhang (lxz79_at_case.edu)
Date: Tue Dec 03 2013 - 14:21:34 CST
Dear NAMD members:
I tried to set up a system including proteins and 1 water molecule. Since
this water molecule is important to keep the protein complex structure, I
need it in setting up my system. After using vmd to add solvent and ions, I
started to run namd simulation on the system. But the simulation crashed
right away by showing the error message like below:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (ATOMS 15956
15958 15957)
In the original pdb file, atoms 15956 and 15957 are the HT and OT atoms of
the water molecule I originally have, while 15958 is the HT atom in the
water molecule added by vmd.
It looks like the vmd did not recognize the water molecule I added thus it
did not set up the correct forcefield parameters for it, although it is a
standard water molecule. I used charmm-27 forcefield parameters. Can anyone
help me on that? Thank you very much.
Best,
Liqun
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