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?
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
