Adding new residue to charmmForcefield

User discussions
1

GROMACS version: 2022
GROMACS modification: Yes
Hello,

I am trying to convert my itp to rtp as to add a new residue to my FF (charm36)
I converted my itp and added it to my rtp

; Name			   
[ AMA ]				

[ atoms ]
;    Atom    type     charge		
     O1      OG311    -0.553    1    ;
     O2      OG2D1    -0.548    2    ;
     N1      NG321    -1.077    3    ;
     N2      NG2D1    -0.824    4    ;
     N3      NG301    -0.137    5    ;
     N4      NG321    -0.502    6    ;
     C1      CG321    -0.281    7    ;
     C2      CG321    -0.196    8    ;
     C3      CG311     0.326    9    ;
     C4      CG321     0.015  10    ;
     C5      CG2O2     0.779  11    ;
     C6      CG2N1     0.500  12    ;
     C7      CG331    -0.207  13    ;
     C8      CG331    -0.207  14    ;
     H1       HGA2     0.090  15    ;
     H2       HGA2     0.090  16    ;
     H3       HGA2     0.090  17    ;
     H4       HGA2     0.090  18    ;
     H5       HGA1     0.090  19    ;
     H6       HGA2     0.090  20    ;
     H7       HGA2     0.090  21    ;
     H8     HGPAM2     0.396  22    ;
     H9     HGPAM2     0.396  23    ;
    H10       HGA3     0.090   24    ;
    H11       HGA3     0.090   25    ;
    H12       HGA3     0.090   26    ;
    H13       HGA3     0.090   27    ;
    H14       HGA3     0.090   28    ;
    H15       HGA3     0.090   29    ;
    H16     HGPAM2     0.330   30    ;
    H17     HGPAM2     0.330   31    ;
    H18       HGP1     0.290   32    ;

then when I run pdb2gmx the pdb coordnates dont match the rtp

Program:     gmx pdb2gmx, version 2022
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 873)

Fatal error:
Atom C in residue AMA 130 was not found in rtp entry AMA with 32 atoms
while sorting atoms.

can someone help me understand how to add a new residue

ama
ama1716×957 269 KB

pdb

ATOM    833  O1  AMA A 133      -4.082  -0.118  -1.252  1.00  0.00           O
ATOM    834  O2  AMA A 133      -3.776  -0.825   0.814  1.00  0.00           O
ATOM    835  N1  AMA A 133      -2.586   1.978   0.882  1.00  0.00           N
ATOM    836  N2  AMA A 133       1.828  -1.071   0.125  1.00  0.00           N
ATOM    837  N3  AMA A 133       3.317   0.328  -0.198  1.00  0.00           N
ATOM    838  N4  AMA A 133       2.932  -1.150   1.185  1.00  0.00           N
ATOM    839  C1  AMA A 133      -0.991   0.166   0.328  1.00  0.00           C
ATOM    840  C2  AMA A 133      -0.503  -0.790  -0.788  1.00  0.00           C
ATOM    841  C3  AMA A 133      -2.305   0.885  -0.063  1.00  0.00           C
ATOM    842  C4  AMA A 133       0.581  -1.776  -0.300  1.00  0.00           C
ATOM    843  C5  AMA A 133      -3.476  -0.083  -0.098  1.00  0.00           C
ATOM    844  C6  AMA A 133       2.753  -0.486   0.318  1.00  0.00           C
ATOM    845  C7  AMA A 133       4.796   0.514  -0.140  1.00  0.00           C
ATOM    846  C8  AMA A 133       2.662   1.663  -0.302  1.00  0.00           C
ATOM    847  H1  AMA A 133      -0.218   0.910   0.528  1.00  0.00           H
ATOM    848  H2  AMA A 133      -1.147  -0.390   1.256  1.00  0.00           H
ATOM    849  H3  AMA A 133      -1.344  -1.383  -1.156  1.00  0.00           H
ATOM    850  H4  AMA A 133      -0.129  -0.210  -1.636  1.00  0.00           H
ATOM    851  H5  AMA A 133      -2.200   1.317  -1.064  1.00  0.00           H
ATOM    852  H6  AMA A 133       0.191  -2.356   0.542  1.00  0.00           H
ATOM    853  H7  AMA A 133       0.826  -2.468  -1.110  1.00  0.00           H
ATOM    854  H8  AMA A 133      -3.478   2.412   0.646  1.00  0.00           H
ATOM    855  H9  AMA A 133      -1.875   2.701   0.809  1.00  0.00           H
ATOM    856  H10 AMA A 133       5.131   1.193  -0.930  1.00  0.00           H
ATOM    857  H11 AMA A 133       5.307  -0.443  -0.277  1.00  0.00           H
ATOM    858  H12 AMA A 133       5.085   0.932   0.830  1.00  0.00           H
ATOM    859  H13 AMA A 133       2.631   2.148   0.680  1.00  0.00           H
ATOM    860  H14 AMA A 133       1.641   1.564  -0.681  1.00  0.00           H
ATOM    861  H15 AMA A 133       3.210   2.309  -0.995  1.00  0.00           H
ATOM    862  H16 AMA A 133       2.885  -1.504   2.139  1.00  0.00           H
ATOM    863  H17 AMA A 133       3.597  -1.743   0.690  1.00  0.00           H
ATOM    864  H18 AMA A 133      -4.815  -0.755  -1.160  1.00  0.00           H
2

This is identical to your other issue: New residue top

Note, too, that using the atom name O2 is going to cause problems, because pdb2gmx is going to translate it to OXT and try to terminate the chain. Use a different name. O1 may also be problematic, check xlateat.dat in $GMXLIB.

3

Thank you
I now have a complete model and have renamed my atoms
pdb

ATOM   1648  N   AMA A 133       5.590  58.089   0.490  1.00 48.56           N  
ATOM   1649  CA  AMA A 133       5.170  59.183   1.347  1.00 48.56           C  
ATOM   1650  C   AMA A 133       5.848  60.488   0.954  1.00 48.56           C  
ATOM   1651  O   AMA A 133       5.182  61.513   0.802  1.00 48.56           O  
ATOM   1652  CB  AMA A 133       5.443  58.855   2.817  1.00 57.81           C  
ATOM   1653  CG  AMA A 133       4.451  57.855   3.410  1.00 57.81           C  
ATOM   1654  CD  AMA A 133       4.497  57.861   4.930  1.00 57.81           C  
ATOM   1655  NE  AMA A 133       5.783  57.394   5.439  1.00 57.81           N  
ATOM   1656  CZ  AMA A 133       6.143  56.118   5.501  1.00 57.81           C  
ATOM   1657  NH1 AMA A 133       5.312  55.173   5.091  1.00 57.81           N1+
ATOM   1658  NH2 AMA A 133       7.337  55.789   5.966  1.00 57.81           N  
ATOM   1659  CQ1 AMA A 133       7.737  54.376   6.031  0.00  0.00           C  
ATOM   1660  CQ2 AMA A 133       8.264  56.837   6.418  0.00  0.00           C  
ATOM   1661  HA  AMA A 133       4.096  59.313   1.215  1.00 48.56           H  
ATOM   1662  H03 AMA A 133       5.744  61.573   0.932  1.00 48.56           H  
ATOM   1663  HB1 AMA A 133       4.996  61.639  -0.131  1.00 48.56           H  
ATOM   1664  HB2 AMA A 133       5.338  59.783   3.378  1.00 57.81           H  
ATOM   1665  HD1 AMA A 133       6.446  58.437   2.898  1.00 57.81           H  
ATOM   1666  HD2 AMA A 133       4.722  56.858   3.063  1.00 57.81           H  
ATOM   1667  HG1 AMA A 133       3.445  58.117   3.084  1.00 57.81           H  
ATOM   1668  HG2 AMA A 133       3.725  57.183   5.293  1.00 57.81           H  
ATOM   1669  H11 AMA A 133       4.325  58.877   5.284  1.00 57.81           H  
ATOM   1670  H12 AMA A 133       4.473  55.599   4.723  1.00 57.81           H  
ATOM   1671  H1  AMA A 133       5.755  54.625   4.368  1.00 57.81           H  
ATOM   1672  H2  AMA A 133       6.054  57.286   0.891  1.00 48.56           H  
ATOM   1673  H3  AMA A 133       5.072  54.575   5.868  1.00 57.81           H  
ATOM   1674  H4  AMA A 133       7.998  54.041   5.070  0.00  0.00           H  
ATOM   1675  H5  AMA A 133       8.596  56.615   7.389  0.00  0.00           H  
ATOM   1676  H6  AMA A 133       6.938  53.802   6.397  0.00  0.00           H  
ATOM   1677  H7  AMA A 133       7.771  57.764   6.419  0.00  0.00           H  
ATOM   1678  H8  AMA A 133       8.562  54.275   6.672  0.00  0.00           H  
ATOM   1679  H9  AMA A 133       9.087  56.879   5.768  0.00  0.00           H

I rewrote my AMA rtp based on arg and 2mr
I dont understand the code of the hbd.dat

I am working on a nontraditional residues guide do you know of other helpful material beyond the manual?

I tried copying and renaming the arginine hbd as AMA and I still cant generate a .gro despite my pdb

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2022
Source file: src/gromacs/gmxpreprocess/add_par.cpp (line 165)

Fatal error:
Atom HH11 not found in rtp database in residue AMA, it looks a bit like HN

my rtp

 [ atoms ]
        N      NH1 -0.4700   1; peptide nitrogen
       HN        H  0.3100   1;polar H
       CA      CT1  0.0700   1; aliphatic sp3 C for CH
       HA      HB1  0.0900   1; backbone H
       CB      CT2 -0.1800   2;aliphatic sp3 C for CH2
      HB1      HA2  0.0900   2; alkane, CH2, new LJ params
      HB2      HA2  0.0900   2;alkane, CH2, new LJ params
       CG      CT2 -0.1800   3;aliphatic sp3 C for CH2
      HG1      HA2  0.0900   3;alkane, CH2, new LJ params
      HG2      HA2  0.0900   3;alkane, CH2, new LJ params
       CD      CT2  0.2000   4;aliphatic sp3 C for CH2
      HD1      HA2  0.0900   4;alkane, CH2, new LJ params
      HD2      HA2  0.0900   4;alkane, CH2, new LJ params
       NE      NC2 -0.7000   4;guanidinium nitrogen
       HE       HC  0.4400   4;N-ter H
       CZ        C  0.6400   4;carbonyl C, peptide backbone
      NH1      NC2 -0.8000   4;guanidinium nitrogen
      H11       HC  0.4600   4;N-ter H
      NH2      NC2 -0.8000   4;guanidinium nitrogen
      CQ1    CG334  0.1100   4;aliphatic C for methyl group (-CH3
       H1     HGA3  0.0900   4;alphatic proton, CH3
       H2     HGA3  0.0900   4;alphatic proton, CH3
       H3     HGA3  0.0900   4;alphatic proton, CH3
      CQ2    CG334  0.1100   4;aliphatic C for methyl group (-CH3
       H4     HGA3  0.0900   4;alphatic proton, CH3
       H5     HGA3  0.0900   4;alphatic proton, CH3
       H6     HGA3  0.0900   4;alphatic proton, CH3  
        C        C  0.5100   5; carbonyl C, peptide backbone
        O        O -0.5100   5; carbonyl oxygen
4

Please provide the content of your .hdb entry for AMA.

5

aminoacids.hbd

AMA        8
1       1       HN      N       CA      -C     
1       5       HA      CA      N       CB      C      
2       6       HB      CB      CG      CA     
2       6       HG      CG      CB      CD     
2       6       HD      CD      CG      NE     
1       1       HE      NE      CZ      CD     
2       3       HH1     NH1     CZ      NH2    
2       3       HH2     NH2     CZ      NH1

also how do I correctly add the bonds angles and dihedrals. my AMA only contains atoms and types

6

Let me save you some work - your residue is already in the CHARMM force field as residue DA2.

As for the core questions:

Only bonds are mandatory to specify; pdb2gmx works out the angles and dihedrals based on bonded connectivity. You simply specify which atoms are bonded. This is fairly simple for a slight modification of an existing residue, you just update those bonds. CHARMM also requires a [cmap] directive, but that’s boilerplate since it’s the same for all residues (unless you’re toying with the backbone, but that’s not relevant here).

As for the .hdb file, again work from an existing residue if possible, and make small adjustments. The issue with your file is that you are specifying that two H atoms will be added to NH1, and they have the base name of HH1. So pdb2gmx will then build on HH11 and HH12. You have neither in your .rtp file, and the PDB coordinates have entirely different names, except H11 and H12 but they’re both connected to entirely different atoms when I visualize the coordinates you provided. That coordinate file is a total mess though, with a strained geometry and very haphazard atom naming. I don’t know how to work off of that, and would suggest rebooting and making all nomenclature consistent with a parent ARG residue, then making small adjustments to generate the desired residue. But again, it’s all sort of a moot point because what you need is already in the force field here. Make sure your residue and atom names in the PDB file are consistent with what the .rtp entry expects, and let fly with pdb2gmx. Make sure you are using the July 2021 version of the CHARMM36 port and you’re covered.