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
Hi Elisabeth, I suspect you somehow did something wrong when adding the "cu" file to the MMTK directory. In the 1.7 release candidate there is already a "cu" file in the directory and minimization of your Mol2 proceeds without any error message. That doesn't mean the minimization is right though -- since the AMBER files have no parameters for Cu (and in particular no NONBOND radius) one of the water oxygens moves right on top of the copper. So, if you use the 1.7 version and edit the heme-iron.frcmod file to add in some of your parameters, like so: MASS FE 55.0 CU 63.55 NONBON FE 1.20000 0.05000 0.00000 CU 1.20000 0.05000 0.00000 then the minimization works much better, with very nice octahedral coordination of the copper. BTW, if you really need the other parameters to carry out your research, then you are going to need to run Add Charge, then explicitly add bonds between the copper and the water oxygens, and then minimize. This is because the underlying antechamber program has no capability to compute partial charges or atom types for copper-containing molecules. Chimera never actually sends an isolated copper ion off to antechamber (it just uses the formal charge and sets the atom type to be the same as the element type), but if the copper is bound to other atoms then it would try to send the molecule to antechamber -- and that would fail. Now, whether using charges that were computed in isolation for the various parts is actually a good idea is a separate issue entirely... As an aside, I think you want "DIHEDRAL" not "DIHEDAL" in your parameters file. --Eric On Jan 22, 2013, at 12:39 PM, Elisabeth Ortega wrote:
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
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 ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
participants (3)
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Elaine Meng -
Elisabeth Ortega -
Eric Pettersen