helpAdun - Support: sr #1768, H2O & charmm

 
 
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sr #1768: H2O & charmm

Submitted by:  None
Submitted on:  Tue 25 Sep 2007 02:55:48 PM UTC  
 
Category: NonePriority: 5 - Normal
Severity: 3 - NormalStatus: None
Privacy: PublicAssigned to: None
Originator Email: -unavailable-Open/Closed: Open
Operating System: None

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Tue 25 Sep 2007 07:21:33 PM UTC, 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 25 Sep 2007 06:51:40 PM UTC, 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 25 Sep 2007 03:20:28 PM UTC, 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 25 Sep 2007 02:55:48 PM UTC, 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

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Carbon-Copy List
  • -unavailable- added by jvilla (Posted a comment)
  • -unavailable- added by mjohnston (Posted a comment)
  • -unavailable- added by mjohnston
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    Follows 1 latest change.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 25 Sep 2007 03:20:28 PM UTCmjohnstonCarbon-Copy-=>Added jvilla
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