water-molecules/coordenates

From: jose correa (corrjose_at_gmail.com)
Date: Thu Feb 11 2010 - 13:19:01 CST

Dear All
I am trying to work with a protein that has structural water molecules.
However, I have this error from the psfgen:

Info) VMD for WIN32, version 1.8.6 (April 7, 2007)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Free system memory: 1051MB (51%)
Info) No joysticks found. Joystick interface disabled.
Found 62 plugins or data handlers in directory
 'C:/Program Files/University of Illinois/VMD/plugins/WIN32/molfile'.
1.4.5
reading topology file top_all27_prot_lipid_na.inp
>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
from
>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
and
  \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
  \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
              Alexander D. MacKerell Jr.
                     August 1999
 All comments to ADM jr. email: alex,mmiris.ab.umd.edu
              telephone: 410-706-7442
Created by CHARMM version 27 1
aliasing residue HIS to HSD
aliasing residue HOH to TIP3
aliasing residue ILE atom CD1 to CD
building segment A
reading residues from pdb file protein-C.pdb
extracted 165 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.
ERROR: Missing atoms for bond C(0) N(1) in residue GLN:209
ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
 in residue GLN:209
Warning: explicit angles in residue TIP3:210 will be deleted during
autogeneration
Warning: explicit angles in residue TIP3:211 will be deleted during
autogeneration
Warning: explicit angles in residue TIP3:212 will be deleted during
autogeneration
Warning: explicit angles in residue TIP3:213 will be deleted during
autogeneration
Info: segment complete.
reading coordinates from pdb file protein-C.pdb for segment A
Warning: failed to set coordinate for atom OXT GLN:209 A
Warning: failed to set coordinate for atom O HOH:210 A
Warning: failed to set coordinate for atom O HOH:211 A
Warning: failed to set coordinate for atom O HOH:212 A
Warning: failed to set coordinate for atom O HOH:213 A
Info: guessing coordinates for 1243 atoms (4 non-hydrogen)
Warning: poorly guessed coordinates for 11 atoms (0 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 MET:50 A
Warning: poorly guessed coordinate for atom HT2 MET:50 A
Warning: poorly guessed coordinate for atom HT3 MET:50 A
Warning: poorly guessed coordinate for atom HG LEU:63 A
Warning: poorly guessed coordinate for atom HG LEU:68 A
Warning: poorly guessed coordinate for atom HG LEU:74 A
Warning: poorly guessed coordinate for atom HG LEU:101 A
Warning: poorly guessed coordinate for atom HG LEU:102 A
Warning: poorly guessed coordinate for atom HG LEU:104 A
Warning: poorly guessed coordinate for atom HG LEU:158 A
Warning: poorly guessed coordinate for atom HG LEU:172 A
Warning: failed to guess coordinates for 12 atoms
Info: writing pdb file protein-C-1.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
Info: writing psf file protein-C-1.psf
total of 2478 atoms
total of 2500 bonds
total of 4515 angles
total of 6592 dihedrals
total of 440 impropers
total of 0 cross-terms
Info: psf file complete.
Info) VMD for WIN32, version 1.8.6 (April 7, 2007)
Info) Exiting normally.
vmd > A:50
Missing atoms for conformation definition
Missing atoms for conformation definition
Missing atoms for conformation definition
Could you have any suggestion or clue to solve this problem?, as you can
see, the water molecules do not have coordenates.

Best wishes
José

-- 
Ph.D. JOSE CORREA BASURTO Professor of Pharmacology, Department of
Biochemistry and Pharmacology, Escuela Superior de Medicina, Instituto
Politécnico Nacional, México. Plan de San Luis Y diaz Mirón S/N, Col. Casco
de Santo Tomas, Mexico city, México. CP: 11340. Tel/Fax; (+5255) 57296000
Ext 62747 and 62767 e:mail: josecorreabasurto_at_hotmail.com or jcorreab_at_ipn.mx,
corrjose_at_gmail.com
website: http://farmacologiacomputacional.blogspot.com/

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:43 CST