[gmx-users] fatal error

[Mark Abraham]

Hi,

What name does the .rtp entry for DC5 use for its phosphorus atom?

Mark

On Mon, Mar 6, 2017 at 1:39 PM Urszula Uciechowska <
urszula.uciechowska at biotech.ug.edu.pl> wrote:

> Dear gmx users,
>
> After running a pdb2gmx script of the pdb file I am getting an error
> message:
>
>
> Fatal error:
> Atom P in residue DC 2 was not found in rtp entry DC5 with 28 atoms
> while sorting atoms.
>
>
> The DC 2 in pdb file:
>
> TER   11412      LEU B 366
> ATOM  11413  P   DC  C   2       0.997  17.702   5.368  1.00 77.21
>   P
> ATOM  11414  OP1 DC  C   2      -0.278  17.623   4.612  1.00 76.82
>   O
> ATOM  11415  OP2 DC  C   2       1.374  16.596   6.287  1.00 76.77
>   O
> ATOM  11416  O5' DC  C   2       2.181  17.899   4.319  1.00 75.66
>   O
> ATOM  11417  C5' DC  C   2       2.302  19.107   3.565  1.00 72.46
>   C
>
> What can be wrong with the P atom?
>
> Thanks for any suggestions.
>
> best
> Urszula Uciechowska
>
>
>
>
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