I suggest you may find solution outside Gromacs. Use Pymol or other
software to simply add hydrogen. Check it (usually they will ignore some
double bonds) and put it back to GROMACS.
Regards,
Yang Ye
On 4/23/2007 5:24 PM, Stas Bobritsky wrote:
Hi all!
I`m working on tRNA MD. My structure contains modified base 2MG, which
have been added to the ffamber99p.rtp:
[2MG]
[atoms]
P amber99_46 1.08783 1
O1P amber99_45 -0.76666 2
O2P amber99_45 -0.76666 3
O5' amber99_44 -0.47131 4
C5' amber99_11 0.06353 5
H5'1 amber99_19 0.06892 6
H5'2 amber99_19 0.06892 7
C4' amber99_11 0.03859 8
O4' amber99_44 -0.32723 9
C1' amber99_11 0.04596 10
C2' amber99_11 0.07745 11
O2' amber99_43 -0.59135 12
HO'2 amber99_25 0.41014 13
H2' amber99_19 0.09290 14
N9 amber99_40 -0.00919 15
C8 amber99_6 0.10447 16
N7 amber99_36 -0.55207 17
C5 amber99_4 0.13484 18
C6 amber99_2 0.58227 19
O6 amber99_41 -0.55183 20
N1 amber99_35 -0.60808 21
C2 amber99_3 0.65874 22
N2 amber99_38 -0.55992 23
H21 amber99_17 0.35843 24
C10 amber99_11 -0.07537 25
H20 amber99_19 0.08216 26
H21 amber99_19 0.08216 27
H22 amber99_19 0.08216 28
N3 amber99_37 - 0.54563 29
C4 amber99_4 0.19346 30
H1 amber99_17 0.34611 31
H8 amber99_24 0.15910 32
H1' amber99_20 0.16432 33
H4' amber99_19 0.11682 34
C3' amber99_11 0.21246 35
H3' amber99_19 0.08253 36
O3' amber99_44 -0.48898 37
[bonds]
...
...
After pdb2gmx -f trna.pdb -o trna.gro -v Gromacs says:
WARNING: atom H5'1 is missing in residue 2MG 1 in the pdb file
You might need to add atom H5'1 to the hydrogen database of
residue 2MG
in the file ff???.hdb (see the manual)
WARNING: atom H5'2 is missing in residue 2MG 1 in the pdb file
You might need to add atom H5'2 to the hydrogen database of
residue 2MG
in the file ff???.hdb (see the manual)
...
...
I try to study hdb file by comparing .rtp, .pdb, and .hdb- entries,
but my PDB structure does not contain any H-atoms.
Where can I read about .hdb entry format for AMBER forcefield?
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