From: Vibhor Agrawal (vibhora_at_g.clemson.edu)
Date: Sat Jun 15 2013 - 21:18:13 CDT
Hello all I was creating a psf for my protein and have capped it with the
ACP and CT1.
When the segment is prepared its giving me following error which I haven't
seen before .Please help.
psfgen) building segment CB1
psfgen) reading residues from pdb file cb1.pdb
psfgen) extracted 301 residues from pdb file
psfgen) setting patch for first residue to ACP
psfgen) setting patch for last residue to CT1
psfgen) Info: generating structure...psfgen) Info: skipping improper
N-C-CA-CD at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-CD at beginning of segment.
psfgen) ERROR: Missing atoms for bond C(0) N(1) in residue CYS:300
psfgen) ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
in residue CYS:300
psfgen) Warning: missing atoms for conformation CYS CA-C-N-CA; skipping.
psfgen) Warning: missing atoms for conformation CYS N-CA-C-O; skipping.
psfgen) Warning: missing atoms for conformation CYS N-CA-C-N; skipping.
segment complete.
below is code which I used:
package require psfgen
topology ./../topology/top_all27_prot_lipid.rtf
pdbalias atom CYS HG HG1
pdbalias residue PLM PALM
pdbalias residue HOH TIP3
pdbalias atom HOH O OH2
pdbalias atom ILE CD1 CD
pdbalias residue HIS HSE
foreach S {cb1} {
segment $S {pdb $S.pdb
first ACP
last CT1
}}
coordpdb cb1.pdb $S
guesscoord
writepsf cb1.psf
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