Dear Chimera dev. team, I have to use my own set of Amber99 parameters because I'm working with transition metals. I'm testing if I can minimize a benchmark system that contains one copper atom coordinated to 6 water molecules. To do it, I don't use any script, I use directly the tool "minimize" present in Tools-> Structure Editing. To do so I edited the frcmod.ff99SB file with the atom, bond, dihedral... all the fields that frcmod.ff99SB ask to me. That didn't work (Element "Cu" is not currently supported by MMTK). Then I followed the instructions here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.h... and I put a file called "cu" with the required data in: lib/python*/site-packages/MMTK/Database/Atoms I tried again, and the same problem. In the same webpage, there are instructions of how can we edit the Amber parameters files present in: bin/amber11/dat/leap/parm I put my parameters in frcmod.ff99SB and I also tried to put it in frcmod.ff03, but it fails again. How can I solve this problem and perform the minimizations? I'm using both windows(x64) and linux(x86) versions of Chimera 1.6.2 (build 36855) but I planned to finish the testing with Chimera 1.7 that contains by default the Amber12 package. At the bottom of the message there is the mol2 file and the parameters that I'm testing. Thanks in advance for your time. Elisabeth O.-C. My mol2 file is: @<TRIPOS>MOLECULE cuh2o.mol2 19 12 1 0 0 SMALL AMBER ff99SB @<TRIPOS>ATOM 1 CU 0.0581 0.0224 0.0049 CU 1 UNK 2.0000 2 OH -2.2040 0.0438 0.0019 O.3 1 UNK -0.8230 3 OH -0.0067 -0.2388 2.1919 O.3 1 UNK -0.8370 4 OH 0.0041 0.2849 -2.1820 O.3 1 UNK -0.8450 5 OH 2.2006 0.0021 0.0073 O.3 1 UNK -0.8270 6 OH -0.0248 -2.4186 -0.2871 O.3 1 UNK -0.8330 7 OH 0.0202 2.4645 0.2971 O.3 1 UNK -0.8420 8 H15 -2.6953 -0.0699 0.6640 H 1 UNK 0.4010 9 H16 -0.6665 -0.1584 2.6929 H 1 UNK 0.4170 10 H18 -0.6618 0.2534 -2.6804 H 1 UNK 0.4330 11 H19 2.6899 -0.0779 -0.6612 H 1 UNK 0.4240 12 H20 0.6422 -2.9163 -0.2996 H 1 UNK 0.4180 13 H14 0.6417 2.9769 0.0874 H 1 UNK 0.4200 14 H17 -2.6936 -0.1186 -0.6513 H 1 UNK 0.4180 15 H22 0.6497 -0.1530 2.6964 H 1 UNK 0.4220 16 H21 0.6504 0.1511 -2.6890 H 1 UNK 0.4130 17 H13 2.6872 -0.2103 0.6483 H 1 UNK 0.4060 18 H24 -0.6602 -2.9263 -0.1105 H 1 UNK 0.4160 19 H23 -0.6488 2.9572 0.3459 H 1 UNK 0.4200 @<TRIPOS>BOND 1 18 6 1 2 14 2 1 3 10 4 1 4 9 3 1 5 8 2 1 6 19 7 1 7 6 12 1 8 17 5 1 9 16 4 1 10 15 3 1 11 13 7 1 12 5 11 1 @<TRIPOS>SUBSTRUCTURE 1 UNK 1 RESIDUE 4 A UNK 0 ROOT And my initial trial of parameters that I write in the mod file is (I put the same than Fe atom parameters written in the file frcmod.heme_ff94 only to test if that works): MASS CU 63.55 BOND CU-OH 200.00 2.0 ANGLE CU-OH-HO 35.00 120.00 OH-CU-OH 50.00 90.00 DIHEDAL X-OH-CU-X 1 0.00 0.00 2.0 NONBON CU 1.2 0.05 0.00 -- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona Tel.: +34935812857 email.: ortega.elisabeth@qf.uab.cat