[gmx-users] adding mdp to amber99sb

[Irem Altan]

Hi,

I am trying to add MPD to the amber99sb forcefields. I have added the necessary things to aminoacids.rtp, aminoacids.hdp, and atomtypes.atp, but when I run pdb2gmx I get the following error:

Fatal error:
Atom type H11 (residue MPD) not found in atomtype database

I’m a bit confused, as I’d have thought H11 would be the atom name and not the atom type because my aminoacids.rtp file contains

[ MPD ]
 [ atoms ]
     C    C1          -0.18000    1
    H1   H11           0.06000    1
    H1   H12           0.06000    1
    H1   H13           0.06000    1
     C    C2           0.26500    1
     O    O2          -0.68300    1
     H    H2           0.41800    1
     C    CM          -0.18000    1
    HM   HM1           0.06000    1
    HM   HM2           0.06000    1
    HM   HM3           0.06000    1
     C    C3          -0.12000    1
    H3   H31           0.06000    1
    H3   H32           0.06000    1
     C    C4           0.14500    1
     O    O4          -0.68300    1
    H4   H41           0.41800    1
    H4   H42           0.12000    1
     C    C5          -0.18000    1
    H5   H51           0.06000    1
    H5   H52           0.06000    1
    H5   H53           0.06000    1
 [ bonds ]
    C1   H11
    C1   H12
    C1   H13
    C1    C2
    C2    O2
    C2    CM
    O2    H2
    CM   HM1
    CM   HM2
    CM   HM3
    C2    C3
    C3   H31
    C3   H32
    C3    C4
    C4    H4
    C4    O4
    O4    H4
    C4    C5
    C5   H51
    C5   H52
    C6   H53

I have added the following to atomtypes.atp:

H1                 1.00800
H2                 1.00800
HM                 1.00800
H3                 1.00800
H4                 1.00800
H5                 1.00800
O2                16.00000
O4                16.00000
C1                12.01000
C2                12.01000
C3                12.01000
C4                12.01000
C5                12.01000

and the aminoacids.hdb:

MPD     14
1	2	H4	O4	C4      C3
1	2	H2	O2	C2	CM
3	4	H5      C5      C4	O4
3	4	HM      CM      C2	C3
3       4	H1	C1	C2	C3
2	6	H3      C3      C4	C2
1	5	H4	C4	C5      C3	O4

I have also added the name to the residuetypes.dat file.

What am I overlooking?

Best,
Irem