From: Pavan (pavan.namd_at_gmail.com)
Date: Fri Dec 06 2013 - 08:03:31 CST
Try removing HT [15956]. This way you only have your protein and the Oxygen
atom [OT] - in separate segments. VMD should recognize this.
Also the force field you are using seems to require an HT-HT bond. Check
and ensure that the topology file used for building in VMD matches the
parameter file used in md.
hth
Pavan
On Tue, Dec 3, 2013 at 3:21 PM, Liqun Zhang <lxz79_at_case.edu> wrote:
> 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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