[chimera-dev] Add new Amber parameters

[Elisabeth Ortega]

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

Tel.: +34935812857
email.: ortega.elisabeth at qf.uab.cat
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