Re: water-molecules/coordenates

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Feb 12 2010 - 12:20:25 CST

Sorry, I guess we should both read the Psfgen manual. :)

It should be pdbalias atom TIP3 O OH2

On Feb 11, 2010, at 4:10 PM, jose correa wrote:

> 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
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:46 CST