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

Mark Abraham mark.j.abraham at gmail.com
Thu Dec 14 10:24:27 CET 2017


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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