From: santanu chatterjee (santanu_c10_at_yahoo.co.in)
Date: Tue Oct 18 2005 - 01:55:39 CDT
Hi
I was trying to create the PSF structure with ww
domain protein. I got the PDB and I used to following
.pgn file to create the PSF structure:
package require psfgen
topology top_all27_prot_lipid.inp
alias residue HIS HSE
alias atom ILE CD1 CD
segment U { pdb ww_domain_1p.pdb }
coordpdb ww_domain_1p.pdb U
guesscoord
writepdb wwd.pdb
writepsf wwd.psf
I ran the following command :
>vmd -dispdev text -e pgnfile
I got the final PDB and PSF but with the following
output/warning:
aliasing residue HIS to HSE
aliasing residue ILE atom CD1 to CD
building segment U
reading residues from pdb file ww_domain_1p.pdb
extracted 39 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of
segment.
Info: skipping conformation C-N-CA-C at beginning of
segment.
Info: skipping conformation C-CA-N-HN at beginning of
segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of
segment.
Info: skipping conformation N-CA-C-O at end of
segment.
Info: skipping conformation N-CA-C-N at end of
segment.
Info: segment complete.
reading coordinates from pdb file ww_domain_1p.pdb for
segment U
Warning: failed to set coordinate for atom 1H LYS:1
U
Warning: failed to set coordinate for atom 2H LYS:1
U
Warning: failed to set coordinate for atom 3H LYS:1
U
Warning: failed to set coordinate for atom 1HB LYS:1
U
Warning: failed to set coordinate for atom 2HB LYS:1
U
Warning: failed to set coordinate for atom 1HG LYS:1
U
Warning: failed to set coordinate for atom 2HG LYS:1
U
Warning: failed to set coordinate for atom 1HD LYS:1
U
Warning: failed to set coordinate for atom 2HD LYS:1
U
Warning: failed to set coordinate for atom 1HE LYS:1
U
Warning: failed to set coordinate for atom 2HE LYS:1
U
Warning: failed to set coordinate for atom 1HZ LYS:1
U
Warning: failed to set coordinate for atom 2HZ LYS:1
U
Warning: failed to set coordinate for atom 3HZ LYS:1
U
Warning: failed to set coordinate for atom H LEU:2
U
Warning: failed to set coordinate for atom 1HB LEU:2
U
Warning: failed to set coordinate for atom 2HB LEU:2
U
Warning: failed to set coordinate for atom 1HD1 LEU:2
U
Warning: failed to set coordinate for atom 2HD1 LEU:2
U
Warning: failed to set coordinate for atom 3HD1 LEU:2
U
Warning: failed to set coordinate for atom 1HD2 LEU:2
U
Warning: failed to set coordinate for atom 2HD2 LEU:2
U
Warning: failed to set coordinate for atom 3HD2 LEU:2
U
Warning: failed to set coordinate for atom 1HB PRO:3
U
Warning: failed to set coordinate for atom 2HB PRO:3
U
Warning: failed to set coordinate for atom 1HG PRO:3
U
Warning: failed to set coordinate for atom 2HG PRO:3
U
Warning: failed to set coordinate for atom 1HD PRO:3
U
Warning: failed to set coordinate for atom 2HD PRO:3
U
Warning: failed to set coordinate for atom 1HB PRO:4
U
Warning: failed to set coordinate for atom 2HB PRO:4
U
Warning: failed to set coordinate for atom 1HG PRO:4
U
Warning: failed to set coordinate for atom 2HG PRO:4
U
Warning: failed to set coordinate for atom 1HD PRO:4
U
Warning: failed to set coordinate for atom 2HD PRO:4
U
Warning: failed to set coordinate for atom H GLY:5
U
Warning: failed to set coordinate for atom 1HA GLY:5
U
Warning: failed to set coordinate for atom 2HA GLY:5
U
Warning: failed to set coordinate for atom H TRP:6
U
Warning: failed to set coordinate for atom 1HB TRP:6
U
Warning: failed to set coordinate for atom 2HB TRP:6
U
Warning: failed to set coordinate for atom H GLU:7
U
Warning: failed to set coordinate for atom 1HB GLU:7
U
Warning: failed to set coordinate for atom 2HB GLU:7
U
Warning: failed to set coordinate for atom 1HG GLU:7
U
Warning: failed to set coordinate for atom 2HG GLU:7
U
Warning: failed to set coordinate for atom H LYS:8
U
Warning: failed to set coordinate for atom 1HB LYS:8
U
Warning: failed to set coordinate for atom 2HB LYS:8
U
Warning: failed to set coordinate for atom 1HG LYS:8
U
Warning: failed to set coordinate for atom 2HG LYS:8
U
Warning: failed to set coordinate for atom 1HD LYS:8
U
Warning: failed to set coordinate for atom 2HD LYS:8
U
Warning: failed to set coordinate for atom 1HE LYS:8
U
Warning: failed to set coordinate for atom 2HE LYS:8
U
Warning: failed to set coordinate for atom 1HZ LYS:8
U
Warning: failed to set coordinate for atom 2HZ LYS:8
U
Warning: failed to set coordinate for atom 3HZ LYS:8
U
Warning: failed to set coordinate for atom H ARG:9
U
Warning: failed to set coordinate for atom 1HB ARG:9
U
Warning: failed to set coordinate for atom 2HB ARG:9
U
Warning: failed to set coordinate for atom 1HG ARG:9
U
Warning: failed to set coordinate for atom 2HG ARG:9
U
Warning: failed to set coordinate for atom 1HD ARG:9
U
Warning: failed to set coordinate for atom 2HD ARG:9
U
Warning: failed to set coordinate for atom 1HH1 ARG:9
U
Warning: failed to set coordinate for atom 2HH1 ARG:9
U
Warning: failed to set coordinate for atom 1HH2 ARG:9
U
Warning: failed to set coordinate for atom 2HH2 ARG:9
U
Warning: failed to set coordinate for atom H
MET:10 U
Warning: failed to set coordinate for atom 1HB
MET:10 U
Warning: failed to set coordinate for atom 2HB
MET:10 U
Warning: failed to set coordinate for atom 1HG
MET:10 U
Warning: failed to set coordinate for atom 2HG
MET:10 U
Warning: failed to set coordinate for atom 1HE
MET:10 U
Warning: failed to set coordinate for atom 2HE
MET:10 U
Warning: failed to set coordinate for atom 3HE
MET:10 U
Warning: failed to set coordinate for atom H
SER:11 U
Warning: failed to set coordinate for atom 1HB
SER:11 U
Warning: failed to set coordinate for atom 2HB
SER:11 U
Warning: failed to set coordinate for atom HG
SER:11 U
Warning: failed to set coordinate for atom H
ARG:12 U
Warning: failed to set coordinate for atom 1HB
ARG:12 U
Warning: failed to set coordinate for atom 2HB
ARG:12 U
Warning: failed to set coordinate for atom 1HG
ARG:12 U
Warning: failed to set coordinate for atom 2HG
ARG:12 U
Warning: failed to set coordinate for atom 1HD
ARG:12 U
Warning: failed to set coordinate for atom 2HD
ARG:12 U
Warning: failed to set coordinate for atom 1HH1
ARG:12 U
Warning: failed to set coordinate for atom 2HH1
ARG:12 U
Warning: failed to set coordinate for atom 1HH2
ARG:12 U
Warning: failed to set coordinate for atom 2HH2
ARG:12 U
Warning: failed to set coordinate for atom H
SER:13 U
Warning: failed to set coordinate for atom 1HB
SER:13 U
Warning: failed to set coordinate for atom 2HB
SER:13 U
Warning: failed to set coordinate for atom HG
SER:13 U
Warning: failed to set coordinate for atom H
SER:14 U
Warning: failed to set coordinate for atom 1HB
SER:14 U
Warning: failed to set coordinate for atom 2HB
SER:14 U
Warning: failed to set coordinate for atom HG
SER:14 U
Warning: failed to set coordinate for atom H
GLY:15 U
Warning: failed to set coordinate for atom 1HA
GLY:15 U
Warning: failed to set coordinate for atom 2HA
GLY:15 U
Warning: failed to set coordinate for atom H
ARG:16 U
Warning: failed to set coordinate for atom 1HB
ARG:16 U
Warning: failed to set coordinate for atom 2HB
ARG:16 U
Warning: failed to set coordinate for atom 1HG
ARG:16 U
Warning: failed to set coordinate for atom 2HG
ARG:16 U
Warning: failed to set coordinate for atom 1HD
ARG:16 U
Warning: failed to set coordinate for atom 2HD
ARG:16 U
Warning: failed to set coordinate for atom 1HH1
ARG:16 U
Warning: failed to set coordinate for atom 2HH1
ARG:16 U
Warning: failed to set coordinate for atom 1HH2
ARG:16 U
Warning: failed to set coordinate for atom 2HH2
ARG:16 U
...and so on. What these warning messages mean? Is it
an error or I can ignore these messages? What can I do
solve this problem? I will appreciate very much if
anyone can give me any advice.
Thanks in advance,
santanu
__________________________________________________________
Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:03 CST