psf generation error

From: Vasumathi Velachi (vas_at_fc.up.pt)
Date: Fri Mar 08 2013 - 13:26:14 CST

Dear All
I am very new to NAMD, I want to simulate cytochrome c, I downloaded
starting structure from protein data bank. I want to add hydrogen atom
and need to create psf file for solvating the molecule. I created
topology file for cytochrome c by merging top_all22_prot.inp and
topology file from this article J Comput Chem 25: 1613–1622, 2004 for
HEME group.
When I am doing so I am getting the some error and warning message and
am getting non-integral charge. when I tried without HEME group the
charge for rest of the system gives me integral charge. Please help me
to solve this issue.
Here is the psfgen file
------------------------
package require psfgen
topology top_all22_prot_heme.rtf
pdbalias residue HEM HEMR
pdbalias residue HIS HSD
pdbalias atom ALA H HN
pdbalias atom ILE CD1 CD
segment U {pdb 1hrc_new.pdb
first ACE}
patch GLUP U:104
patch THI1 U:14 U:105
patch THI2 U:17 U:105
coordpdb 1hrc_new.pdb U
guesscoord
writepdb protein_new_ACE.pdb
writepsf protein_new_ACE.psf
quit
------------------------
Error message
psfgen) Created by CHARMM version 31 1
psfgen) cross-term entries present in topology definitions
psfgen) ERROR! Failed to parse patching statement.
psfgen) ERROR! Failed to parse internal coordinate statement.
psfgen) ERROR! Failed to parse internal coordinate statement.
psfgen) ERROR! Failed to parse internal coordinate statement.
psfgen) ERROR! Failed to parse internal coordinate statement.
psfgen) ERROR! Failed to parse internal coordinate statement.
psfgen) aliasing residue HEM to HEMR
psfgen) aliasing residue HIS to HSD
psfgen) aliasing residue ALA atom H to HN
psfgen) aliasing residue ILE atom CD1 to CD
psfgen) building segment U
psfgen) reading residues from pdb file 1hrc_new.pdb
psfgen) extracted 105 residues from pdb file
psfgen) setting patch for first residue to ACE
psfgen) Info: generating structure...psfgen) Info: skipping improper
N-C-CA-HN at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of
segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
psfgen) ERROR: Missing atoms for bond C(0) N(1) in residue GLU:104
psfgen) ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
         in residue GLU:104
psfgen) ERROR: Missing atoms for cross-term C(-1) N(0) CA(0) C(0) N(0)
CA(0) C(0) N(1)
         in residue GLU:104
psfgen) Warning: missing atoms for conformation GLU CA-C-N-CA;
skipping.
psfgen) Warning: missing atoms for conformation GLU N-CA-C-O; skipping.
psfgen) Warning: missing atoms for conformation GLU N-CA-C-N; skipping.
segment complete.
psfgen) applying patch GLUP to 1 residues
psfgen) applying patch THI1 to 2 residues
psfgen) applying patch THI2 to 2 residues
psfgen) reading coordinates from pdb file 1hrc_new.pdb for segment U
psfgen) Info: guessing coordinates for 884 atoms (3 non-hydrogen)
psfgen) Warning: poorly guessed coordinates for 10 atoms (3
non-hydrogen):
psfgen) Warning: poorly guessed coordinate for atom CAY GLY:1 U
psfgen) Warning: poorly guessed coordinate for atom HY1 GLY:1 U
psfgen) Warning: poorly guessed coordinate for atom HY2 GLY:1 U
psfgen) Warning: poorly guessed coordinate for atom HY3 GLY:1 U
psfgen) Warning: poorly guessed coordinate for atom CY GLY:1 U
psfgen) Warning: poorly guessed coordinate for atom OY GLY:1 U
psfgen) Warning: poorly guessed coordinate for atom HN GLY:1 U
psfgen) Warning: poorly guessed coordinate for atom HE2 GLU:104
  U
psfgen) Warning: poorly guessed coordinate for atom HBA2
HEMR:105 U
psfgen) Warning: poorly guessed coordinate for atom HBD2
HEMR:105 U
psfgen) Info: writing pdb file protein_new_ACE.pdb
----------------------
Thanking you in advance

-- 
Vasumathi Velachi

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