Cofactors vanishing in editconf - Redmine #2900
Archive from user: Erik Marklund
I have a dimeric protein with two cofactors. After getting it through pdb2gmx (with some effort) I obtained a new pdb-file, which I passed on to editconf to get a suitable box. The cofactors however vanished in the editconf ste
I then tried using gromacs 2016.3, and then editconf managed to handle the cofactors. I also noticed some differences in the pdb2gmx step, where 2019.1 required the two cofactors to have different residue numbers, even though they belonged to different chains, whereas 2016 needed no such workaround.
Note that while investigating this issue, we also found that pdb2gmx, solvate and insert-molecules no longer accepted .tpr files as input, which is now fixed.
(from redmine: issue id 2900, created on 2019-03-20 by gmxdefault, closed on 2019-04-15)
- Changesets:
- Revision 69731121 by Berk Hess on 2019-04-15T14:48:54Z:
Fix pdb-related issues
In editconf, if a PDB input was read, chain IDs are known, and should
be written if the output is also PDB. This now works again, after
being broken in commit 8dd3c9ae88004054b3.
This required adding missing tpr support to readConfAndAtoms(), which
also fixes that pdb2gmx, insert-molecules, and solvate could not read
tpr files. Those are the only tools that directly or indirectly called
readConfAndAtoms with a .tpr file.
Fixes #2900
Change-Id: I883777be945023a7e69260b22e76df54477828ee
- Revision 57b3e3d9 by Berk Hess on 2019-04-18T08:57:55Z:
Fix pdb-related issues
In editconf, if a PDB input was read, chain IDs are known, and should
be written if the output is also PDB. This now works again, after
being broken in commit 8dd3c9ae88004054b3.
This required adding missing tpr support to readConfAndAtoms(), which
also fixes that pdb2gmx, insert-molecules, and solvate could not read
tpr files. Those are the only tools that directly or indirectly called
readConfAndAtoms with a .tpr file.
Fix in master also closes memory leaks.
Refs #2900
Change-Id: I883777be945023a7e69260b22e76df54477828ee
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