From: Burgess, Don E (deburgess_at_uky.edu)
Date: Fri Sep 30 2011 - 11:49:26 CDT

When I use the Mutator plugin on a system with a protein embedded in a POPE membrane that uses the recent charm36 lipid ff, it generates a PSF file with extra (Shake) bonds in certain water molecules (in the SOLV segment). Consequently, when I run a simulation with NAMD, I get the error message:

UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT

which has been discussed previously.

I am confused because all of the topology files used by the plugin to generate the psf file have the CORRECT TIP3 residue:

RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
BOND OH2 H1 OH2 H2
ANGLE H1 OH2 H2 ! required
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE

So, I do not understand how the Plugin can generate an incorrect PSF file. The original PSF file has the correct bond structure for the water molecules.

If it would help trouble shoot this problem, please tell me how to submit the relevant PSF files.

thank you very much,
don burgess