From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Oct 18 2005 - 02:09:05 CDT
Unfortunately your pdb uses a nonstandard naming convention for some of the
atoms (apparently most of the hydrogens). For instance, I see 1HG when it
should be HG1. You can determine the names by looking at the topology file.
The way around this is to either edit the pdb manually (time consuming) or
write a significantly longer input script for psfgen that also changes the
name of each of these atoms. For example, you would need:
pdbalias atom LYS 1HB HB1
pdbalias atom LYS 2HB HB2
pdbalias atom LYS 1HG HG1
etc., probably on the order of 100-200 lines.
While most of these are obvious, you should look at the structure in the
topology file and compare it to your structure in VMD to determine the
correct mapping.
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of santanu chatterjee
Sent: Tuesday, October 18, 2005 1:56 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: A question on psfgen
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
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