darianyang / ff15ipq-19f

Scripts and files associated with 19F ff15ipq parameter derivation and validation.

ff15ipq-19F manuscript: scripts and input files

These files are associated with the following publication:

DT Yang, AM Gronenborn, LT Chong, “Integrating Fluorinated, Aromatic Amino Acids into the Framework of the AMBER ff15ipq Force Field.” J. Phys. Chem. A, 2022, in press; https://doi.org/10.1021/acs.jpca.2c00255

• force field parameters for fluorinated amino acids commonly used with ¹⁹F NMR experiments

• see final_parameters/ for the AMBER compatible frcmod (bonded parameters) and leap (ipq charges) files for use with the ff15ipq protein force field, along with instructions for how to use these files
• not all original files were included due to size limitations
  • raw trajectory data is available upon reasonable request: please email [email protected]
• see analysis/ for Python scripts used for analysis and figure generation
• for fluorine relaxation calculations, see https://github.com/darianyang/fluorelax

ff15ipq-19f's Issues

How to use OD atom type for oxygen atom

Hello.
Thanks for sharing these scripts.
I am trying to parameterize norleucine.
I am following the scripts but I have encountered a problem i.e. if I change the atom type of oxygen atom to OD and run parmchk as follows.

parmchk2 -i NLE.mol2 -f mol2 -o NLE.frcmod -p /home/amin/softwares/amber22/dat/leap/parm/parm15ipq_10.3.dat

I get an error

Atom type of OD does not exist in PARMCHK.DAT

If I use atom type O, it works and I get an frcmod file as expected.
Did you encounter this problem as well?
Can you think of something I might be doing wrong?
The atom section of my mol2 is as follows.

@<TRIPOS>ATOM
      1 N           -1.9680     0.0710     0.3120 N          1 NLE      -0.251000
      2 CA          -1.2060     1.2220    -0.1620 CX         1 NLE      -0.054000
      3 C            0.2920     1.0090     0.0910 C          1 NLE       0.216000
      4 O            0.7170     0.4370     1.0960 OD         1 NLE      -0.217000
      5 CB          -1.7010     2.5050     0.5400 2C         1 NLE      -0.190000
      6 CG          -1.3600     3.7940    -0.2280 3C         1 NLE      -0.153000
      7 CD          -1.8050     5.0560     0.5250 CT         1 NLE      -0.159000
      8 CE          -1.6020     6.3320    -0.2980 CT         1 NLE      -0.211000
      9 H           -1.4810    -0.3330     1.1060 H          1 NLE       0.138000
     10 HA          -1.3700     1.3210    -1.2370 H1         1 NLE       0.142000
     11 HB2         -2.7830     2.4620     0.6610 HC         1 NLE       0.095500
     12 HB3         -1.2860     2.5590     1.5490 HC         1 NLE       0.095500
     13 HG2         -1.8470     3.7630    -1.2030 HC         1 NLE       0.084500
     14 HG3         -0.2880     3.8500    -0.4220 HC         1 NLE       0.084500
     15 HD2         -2.8560     4.9750     0.8000 HC         1 NLE       0.079000
     16 HD3         -1.2490     5.1380     1.4590 HC         1 NLE       0.079000
     17 HE1         -1.8950     7.2150     0.2720 HC         1 NLE       0.074000
     18 HE2         -0.5590     6.4580    -0.5890 HC         1 NLE       0.074000
     19 HE3         -2.2040     6.3150    -1.2090 HC         1 NLE       0.074000

I would be really grateful for any suggestions.
Best,
Amin.