From: Shirley Li (li19104_at_yahoo.com)
Date: Thu Dec 22 2005 - 13:16:00 CST
For my problem, I found the solution from NAMD Archive, titled "ATP fix (fwd)" at
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0202.html, by changing the atom types of ATP.
However, the run still crashed with error message of "FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT", which is related to TIP3P water molecules. I wonder what's wrong.
Any help will be appreciated.
Shirley
Shirley Li <li19104_at_yahoo.com> wrote: Thanks Brian and Josh a lot for the kind help. Indeed, there are CN7-type atoms in my .psf file, which belong to ATP.
I wonder why this atom type causes problem. Is the angle parameters for CN7 atom indeed missing in NAMD parameter file, and so it needs to be added manually? I worked on another protein with GTP which also has CN7 atoms, and NAMD didn't complain though.
Any information will be very much appreciated.
Shirley
"Joshua D. Moore" <jdmoore_at_unity.ncsu.edu> wrote: Hi Shirley,
If you get this error, I think you must have CN7 atoms somewhere in your
.psf file. Perhaps you meant to have them as something else? Maybe this
occured as part of your merging?
Josh
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