1. When I convert the pdb file into Cartesian coordinate file using pdbxyz program, irrespective of the force filed used, I get a warning that two of the atoms have the exact same coordinates. Also, two copper atoms in the pdb file are not converted in the Cartesian file. Which might be the best force field to use for this purpose?
2. While using the "minimize" program:
Error: "MECHANIC -- Some Required Potential Energy Parameters are Undefined
TINKER is Unable to Continue; Terminating the Current Calculation"
OR
Error - "GRADIENT -- Illegal Value for the Total Potential Energy
TINKER is Unable to Continue; Terminating the Current Calculation"
It generates a new .xyz file but it doesn't seem any different from the input one.
I have tried using multiple force fileds (amber 94 & 99, oplsaa & oplsaal, charmm22 etc but end up with the first error usually. I crosschecked the xyz file with the parameter file and none of the atom types were missing, though the Cu atoms in the original pdb file are not accounted for,
I am using the Linux executables provided for the program on Ubuntu 14.
Maybe you set a gradient value which is out of the range you can use in TINKER (which is crystal clear in the error) :)
http://www-jmg.ch.cam.ac.uk/cil/tinker/c4.html
Hope this helps.
I have tried the minimizations with different values of the RMS gradient up to 1.0 (0.01 is default). They all return one of the two errors, mostly the former.
Though I have never used TINKER, but warning "two of the atoms have the exact same coordinates" suggests a problem in your structure (may be your copper atoms are overlapping or any other two atoms). Also, There is a high possibility that your PDB structure contain some atoms (most probably Copper metal ions, many force field does not support metal ions) which are not defined in force fields. In that case, you need to hunt for a force filed modified by someone for Copper metal ion or make one yourself.
"Some Required Potential Energy Parameters are Undefined" this also seems to be related to undefined parameters of some atoms (again may be Copper).
In sort...look for force field which support Copper .
Sorted. The two atoms with identical coordinates are hydrogen atoms added by the pdbxyz program to a glutamine residue by way of protein preparation, and not in the original PDB file.
the missing parameters are indeed due to two metal ions present.
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