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
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
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.
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
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.
