[gmx-users] Adding HSD residue to AMBER ff99SB-ILDN

[Simone Bolognini]

Hi everyone,
I have a .pdb file of the WW domain of human FIP35 protein extracted from
an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3.
Now I need to obtain the topology out of it, but the .pdb contains a
residue, namely HSD, which is not present in the Amber residue database. I
looked at the source files and found out that CHARMM has it. In particular,
this is what you can find in the CHARMM database:

[ HSD ]
 [ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.09 4
HB1 HA 0.09 5
HB2 HA 0.09 6
ND1 NR1 -0.36 7
HD1 H 0.32 8
CG CPH1 -0.05 9
CE1 CPH2 0.25 10
HE1 HR1 0.13 11
NE2 NR2 -0.70 12
CD2 CPH1 0.22 13
HD2 HR3 0.10 14
C C 0.51 15
O O -0.51 16
 [ bonds ]
CB CA
CG CB
ND1 CG
CE1 ND1
NE2 CD2
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
ND1 HD1
CD2 HD2
CE1 HE1
O C
CG CD2
CE1 NE2
 [ impropers ]
ND1 CG CE1 HD1
CD2 CG NE2 HD2
CE1 ND1 NE2 HE1
ND1 CE1 CG HD1
CD2 NE2 CG HD2
CE1 NE2 ND1 HE1
N -C CA HN
C CA +N O
 [ cmap ]
-C N CA C +N

Is there any possible way in which I can "copy and paste" this in the Amber
database and hope it will work correctly? Thank you very much!!!