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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