PTools

write pdb charmm format

Bug #708040 reported by Marc Gueroult
12
This bug affects 1 person
Affects Status Importance Assigned to Milestone
PTools
Fix Committed
High
Unassigned
PTools 1.1

Bug Description

when we use PrintPdb or WritePDB, ptools doesn't respect the format atomname with Charmm force field. add a condition in pdbio.cpp for manage the problem.

problem solve in attached file for DNA.

Revision history for this message
Marc Gueroult (marc-gueroult) wrote :
Marc Gueroult (marc-gueroult)
visibility: public → private
Revision history for this message
Adrien Saladin (adrien-saladin) wrote :

We need precisions: can CHARMM read normal PDBs (from RCSB for example)? In other terms is this a bug in PTools that does not write PDB with a correct format or just CHARMM which needs specifically crafted PDBs ?

Changed in ptools:
status: New → Incomplete
visibility: private → public
Revision history for this message
Adrien Saladin (adrien-saladin) wrote :

Indeed it's a PTools bug. Your fix should be applied to all atoms.

While we are at it, a few other fields are not correctly handled. For example the "altLoc".

http://www.wwpdb.org/documentation/format32/sect9.html

Changed in ptools:
status: Incomplete → Confirmed
importance: Undecided → High
milestone: none → 1.1
Adrien Saladin (adrien-saladin)
Changed in ptools:
status: Confirmed → Fix Committed
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