Adding new residue to GMML2: GulNAcA

[gitoliver]

Rajan Kandel has requested the a GulNAcA be added to GMML2. Here is the prep file from Raj:

This is a remark line
molecule.res
UNL   INT  0
CORRECT     OMIT DU   BEG 
  0.0000
   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
   3  DUMM  DU    M    2   1   0     1.523   111.21       .0      .00000
   4  C1    Cg    M    3   2   1     1.540   111.208  -180.000  0.255000
   5  H1    H2    E    4   3   2     1.094   109.276   -97.235  0.000000
   6  C2    Cg    3    4   3   2     1.557   109.045   143.372  0.450000
   7  H2    H1    E    6   4   3     1.098   108.583   170.167  0.000000
   8  N2    Ng    B    6   4   3     1.472   114.150    52.348 -0.672000
   9  H2N   H     E    8   6   4     1.014   114.777  -146.807  0.277000
  10  C2N   C     B    8   6   4     1.377   120.733    64.341  0.669000
  11  CME   Cg    3   10   8   6     1.505   113.960   174.659 -0.004000
  12  H3M   Hc    E   11  10   8     1.092   109.073   150.053  0.000000
  13  H2M   Hc    E   11  10   8     1.095   109.483   -90.310  0.000000
  14  H1M   Hc    E   11  10   8     1.093   111.121    30.886  0.000000
  15  O2N   O     E   10   8   6     1.225   124.331    -4.024 -0.626000
  16  C3    Cg    3    6   4   3     1.545   109.571   -71.578  0.194000
  17  H3    H1    E   16   6   4     1.096   110.670    69.211  0.000000
  18  O3    Oh    S   16   6   4     1.442   109.305  -173.863 -0.692000
  19  H3O   Ho    E   18  16   6     0.983   103.508    86.926  0.407000
  20  C4    Cg    3   16   6   4     1.532   110.033   -53.205  0.261000
  21  H4    H1    E   20  16   6     1.096   110.685  -179.178  0.000000
  22  O4    Oh    S   20  16   6     1.445   105.340   -64.113 -0.720000
  23  H4O   Ho    E   22  20  16     0.996   104.374   151.065  0.427000
  24  C5    Cg    B   20  16   6     1.530   108.512    57.543  0.123000
  25  H5    H1    E   24  20  16     1.098   110.727    61.119  0.000000
  26  C6    C     B   24  20  16     1.545   106.536   178.936  0.886000
  27  O6A   O2    E   26  24  20     1.266   114.998    56.355 -0.825000
  28  O6B   O2    E   26  24  20     1.266   115.052  -119.131 -0.825000
  29  O5    Os    M    4   3   2     1.424   110.426    18.842 -0.391000


LOOP
   O5   C5  

IMPROPER
   C2   H1   C1   O5  
  CME   N2  C2N  O2N 
   C5  O6A   C6  O6B 

DONE
STOP

Note that the residue name UNL is non-standard. Not sure yet if this is alpha or beta. GLYCAM needs one of each.
The following program will find derivatizable positions around the ring (e.g. 2,3,4,6) and generate all the combinations.

Steps (note, any steps that modify .cpp files require a recompile (./make.sh):

1. Add the prep file(s) to gmml2/dat/prep/. You could also copy it into the existing giant prep file and skip step 3, but it's very easy to mess up formatting in a prep file so be careful.
2. Edit gmml2/programs/glycamResidueCombinator.cpp to read in the residue name (UNL).
3. Edit scripts/027.test.glycamResidueCombinator.sh to pass the prep file into to the program.
4. Edit gmml2/src/metadata/glycam06Functions.cpp to add the residue name to the ResidueNameCodeLookup.*
5. Run the program, it should produce a new GLYCAM06.lib file.
6. Replace the lib file here: https://github.com/GLYCAM-Web/gmml2/blob/main/dat/parameters/GLYCAM_06k.lib
7. Diff the the test 27 outputs and if it looks sane, update the outputs so the test passes with the new info.Any new bond, angle, dihedral terms need to be added to MD_Utils so that tleap knows about them.

*e.g:
{ "SUGpa", "EY", "Saccharide"},
{ "SUGpb", "Ey", "Saccharide"},

Replace SUG with your sugar name.

[gitoliver]

LGulpNAcAa1-OH could be built via text in my local dev env on Jan 9th, now waiting for test to be updated:

Note there is no button or plans for a button, only alpha is available.