[gmx-users] Atom HG1 not found in rtp database...

Vishwambhar Bhandare vishwayogi at gmail.com
Thu Dec 14 08:43:48 CET 2017

I get this error while running pdb2gmx,

*"Atom HG1 not found in rtp database in residue PRO, it looks a bit like
the proline is modified,,,In my structure,
'HG1' is replace with 'F'.
The N-terminal and C-terminal are capped with ACE and NH2 respectively...
I tried with OPLS and AMBER ILDN force field..

I modified proline atom in force field file as given below,

[ PRO ]
 [ atoms ]
     N    N           -0.25480     1
    CD    CT           0.01920     2
   HD1    H1           0.03910     3
   HD2    H1           0.03910     4
    CG    CT           0.01890     5
     F    HC           0.02130     6
   HG2    HC           0.02130     7
    CB    CT          -0.00700     8
   HB1    HC           0.02530     9
   HB2    HC           0.02530    10
    CA    CT          -0.02660    11
    HA    H1           0.06410    12
     C    C            0.58960    13
     O    O           -0.57480    14
 [ bonds ]
     N    CD
     N    CA
    CD   HD1
    CD   HD2
    CD    CG
    CG     F
    CG   HG2
    CG    CB
    CB   HB1
    CB   HB2
    CB    CA
    CA    HA
    CA     C
     C     O
    -C     N
 [ impropers ]
    CA    +N     C     O
    -C    CD     N    CA

How this issue can be resolved??

Thanks in advance

Vishwamhbar Bhandare
​Research Associate​
Bose Institute,

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