[gmx-users] Special bond between metallic layers & protein

[Nicola Staffolani]

Ah, I have to write down the old residue instead of leaving the spaces
blank! Like this for a toy pdb file with only 2 platinum atoms it work ;)
meaning that the matrix of the distances between all the special atoms is
constructed, the special atom around the cut-off distance are linked and no
error message is generated ;) But if now I load the true pdb file with 1650
platinum atoms, the distance matrix is again generated *;)* the special
atoms around the cut-off distance are again correctly linked *;) *but then
I get the following error messages:

Making bonds...

WARNING: WARNING: Atom 8�%    H�%    �
 is used in an interaction of type
special bond in the
topology database, but an atom of that name was not found in
residue number 130.

WARNING: WARNING: Atom ��%    ��%    �
 is used in an interaction of type
special bond in the
topology database, but an atom of that name was not found in
residue number 680.

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/pdb2top.c, line:
737

Fatal error:
Trying to make impossible special bond (8�%    H�%    �
-��%    ��%    �
)!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors





-- 
Nicola Staffolani PhD
Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36