Hi
I was trying to load a pdb file and generate the psf file for this pdb. I
was able to load the pdb file using loadPDB-
protocol.loadPDB("2dau.pdb")
Now I try to generate my PSF using the command-
psfGen.pdbToPSF("2dau.pdb")
However I am shown the following error-
%SEGMNT-ERR: attempt to enter duplicate residue A 1 CYT
%SEGMNT-ERR: attempt to enter duplicate residue A 1 GUA
%SEGMNT-ERR: attempt to enter duplicate residue A 1 CYT
%SEGMNT-ERR: attempt to enter duplicate residue A 1 GUA
%SEGMNT-ERR: attempt to enter duplicate residue A 1 ADE
%SEGMNT-ERR: attempt to enter duplicate residue A 1 ADE
%SEGMNT-ERR: attempt to enter duplicate residue A 1 THY
%SEGMNT-ERR: attempt to enter duplicate residue A 1 THY
%SEGMNT-ERR: attempt to enter duplicate residue A 1 CYT
%SEGMNT-ERR: attempt to enter duplicate residue A 1 GUA
%SEGMNT-ERR: attempt to enter duplicate residue A 1 CYT
%SEGMNT-ERR: attempt to enter duplicate residue A 1 GUA
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
%PATCH-ERR: atom O2' not found
Since my pdb file is that of a DNA, I am not sure exactly what to do. Where
do I put in my patch statements for DNA? Or is there any other way to let
psfGen know it is a DNA structure? I will really be glad for any help.
Thank you very much.
Regards
Sudakshina Ganguly
Senior Research Fellow
Department of Biophysics
Bose Institute
India
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