helpAdun - Support: sr #1768, H2O & charmm

Show feedback again

sr #1768: H2O & charmm

Submitted by:  None
Submitted on:  Tue Sep 25 14:55:48 2007  
Category: NonePriority: 5 - Normal
Severity: 3 - NormalStatus: None
Privacy: PublicAssigned to: None
Originator Email: -unavailable-Open/Closed: Open
Operating System: None

Add a New Comment (Rich MarkupRich Markup):

You are not logged in

Please log in, so followups can be emailed to you.


Tue Sep 25 19:21:33 2007, comment #3:

Adun would expect there to be extra angle interactions centered on the H's but I think these are supposed to be there as part of the TIP model. They should be taken care of by making the equilibrium angle equal to the initial angle. In this way the hydrogens should be constrained from moving apart by both the bond between them and the angle constraint. Maybe the inital angle taken from the water pdb is incorrect and this is causing problems. The parameters and interactions adun is calculating should be checked through the SystemAnalysis plugin. I remember that giampi looked into this once.

It also possible that adun is trying to calculate a torsion that doesnt exist due to the extra bond eg. H1, H2, O, H1, but I think this case is handled. Again this can be checked through SystemAnalysis.

Michael Johnston <mjohnston>
Project Administrator
Tue Sep 25 18:51:40 2007, comment #2:

1) then there is perhaps a problem as Adun expects thoe two hydrogens to be part of a bending centered in one of them. If this is not the case here the exception should be taken care of.

2) the solution of changing the 4 letter code to 3 letter code looks good

Jordi VillĂ -Freixa <jvilla>
Project Administrator
Tue Sep 25 15:20:28 2007, comment #1:

1) As far as I know the bond between the two H in TIP3 is there in order to keep it rigid.

2) This is a restriction imposed by the pdb format where residue names may only be 3 characters long. In an effort to enforce standards, reduce errors and reduce the already large amount of special cases that have to be handled explicitly, Adun follows the pdb format rigorously. However as in Charmms case some force-fields assign four letter names to residues which is incompatible with strict parsing of pdbs.

Without updating the parser to allow residue names to encroach into the defined padding area between the residue name and chain id (which won't happen soon) the only way to handle this situation is to rename the residue in the topology file with a unique three letter code.

Michael Johnston <mjohnston>
Project Administrator
Tue Sep 25 14:55:48 2007, original submission:

two little errors by loading a watermolecule with charmm:
1) in the typology file the TIP3-entry for the water contains a connection between the two H
2) only residue names up to 3 digits seem to be possible



(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):

No files currently attached


Depends on the following items: None found

Items that depend on this one: None found


Carbon-Copy List
  • -unavailable- added by jvilla (Posted a comment)
  • -unavailable- added by mjohnston (Posted a comment)
  • -unavailable- added by mjohnston

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only logged-in users can vote.


    Error: not logged in



    Follows 1 latest change.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue Sep 25 15:20:28 2007mjohnstonCarbon-Copy-=>Added jvilla
    Show feedback again

    Back to the top

    Powered by Savane 3.1-cleanup