[chimera-dev] Add new Amber parameters

Tue Jan 22 15:14:41 PST 2013

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.html#limitations
> 
> 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
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