[chimera-dev] Add new Amber parameters

[Elaine Meng]

Just a PS to Eric's reply...

Note that the waters are not treated as standard residues (not assigned the TIP3P water parameters) because in your file, everything is in one residue named UNK.

If you had wanted the waters to get TIP3P parameters, they would need to be separate residues with standard residue and atom names for water.  I read in your Mol2 file, wrote out a PDB file, then hand-edited the PDB: re-ordered the atoms to make 7 separate residues (Cu and 6 waters), renumbered the residues, and renamed the waters to residue name HOH and atom names O,H1,H2.   Resulting PDB file test.pdb attached.

Then I could minimize in 1.7 or pre-1.8 daily build after adding parameters for the copper ion.  Although you could put these in any of the parm files mentioned in the instructions, in my specific tests with the attached PDB file, I just added this one line to the end of frcmod.ionsjc_tip3p:

  CU       1.10      0.0125          ECM test only, values like Zn in parm10.dat

There is already a mass for CU in parm10.dat, and as Eric mentioned, a cu file in the MMTK directory.
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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