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

[Mark Abraham]

Hi,

That can't work if you also have normal proline, which is probably the
problem when you look at the whole context. Makes new one, after searching
Google for the how-to guide.

Mark

On Thu, Dec 14, 2017, 6:44 PM Vishwambhar Bhandare <vishwayogi at gmail.com>
wrote:

> Hi,
> I get this error while running pdb2gmx,
>
>
>
> *"Atom HG1 not found in rtp database in residue PRO, it looks a bit like
> HG2"*
> 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,
> Kolkata-54
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