[gmx-users] fatal error

[Urszula Uciechowska]

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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