Re: water-molecules/coordenates

From: jose correa (corrjose_at_gmail.com)
Date: Thu Feb 11 2010 - 16:10:09 CST

Thank you Gumbart
I have tried as:

pdbalias residue OH2 TIP3
modifiying the *pdb HOH by OH2, but, the error still, I use:

pdbalias atom O OH2
but the error still. other suggestion?, please.
Best wishes
Josť

2010/2/11 JC Gumbart <gumbart_at_ks.uiuc.edu>

> O is not the name of a water oxygen in the Charmm forcefield, OH2 is.
> Therefore, add "pdbalias atom O OH2" to your script.
>
>
> On Feb 11, 2010, at 1:19 PM, jose correa wrote:
>
> 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
> Josť
>
>
>

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