From: Katrin Stöbener (katrin.stoebener_at_itwm.fhg.de)
Date: Fri Oct 19 2012 - 02:30:19 CDT
Dear all,
with the help of psfgen I'd like to build a psf file out of a pdb file I
got from the pdb data bank (Ncbi.pdb):
ATOM 1 CA ALA A 1 2.084 128.960 31.798 1.00
0.00 A
ATOM 2 CA SER A 2 2.887 125.804 29.847 1.00
0.00 A
..
ATOM 130 CA ALA A 1 -38.110 115.198 54.063 1.00
0.00 A
ATOM 131 CA SER A 2 -37.863 112.444 51.463 1.00
0.00 A
..
After separating the file in three different files containing the
different chain informations, I started psfgen:
./psfgen << END
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment A {pdb chainA.pdb}
segment B {pdb chainB.pdb}
segment C {pdb chainC.pdb}
coordpdb chainA.pdb A
coordpdb chainB.pdb B
coordpdb chainC.pdb C
writepdb ms2.pdb
writepsf ms2.psf
END
Now I get the following error message:
duplicate residue key 1
ERROR: failed on residue ALA from pdb file
duplicate residue key 2
ERROR: failed on residue SER from pdb file
..
Do I have to change all of the residue ids or is there a different way
psfgen will accept the pdb file?
Thanks,
Katrin
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