ParmEd/ParmEd issues and pull requests

#1256 - Fix bond order assignment in structure copying and slicing

Pull Request - State: closed - Opened by swails almost 2 years ago - 1 comment

#1255 - Structure.copy() does not carry bond orders

Issue - State: closed - Opened by sebastianmdick about 2 years ago - 1 comment

#1254 - Export openMM system with tip4pew water to GROMACS top/gro

Issue - State: open - Opened by maxbonomi about 2 years ago - 3 comments
Labels: bug

#1253 - Charges from an OpenMM topology/system don't apply to atomtypes

Issue - State: open - Opened by umesh-timalsina about 2 years ago - 1 comment

#1252 - Add an RDKit export utility

Pull Request - State: closed - Opened by swails about 2 years ago

#1251 - A large potential energy difference between GROMACS-2021.4 and OpenMM-7.6.0

Issue - State: open - Opened by Dropletsimuli about 2 years ago

#1250 - Merge more than one ligand into protein with conflicting atomtypes will silently overwrite the atomtypes

Issue - State: open - Opened by xiki-tempula about 2 years ago

#1249 - pip install ParmEd gettting error jupyter notebook

Issue - State: closed - Opened by imrbay about 2 years ago - 1 comment

#1248 - Error writing out prmtop file from OpenMM system

Issue - State: closed - Opened by connormorris1 about 2 years ago - 2 comments

#1247 - error when reading ff14idpff top

Issue - State: closed - Opened by JaimeRubioMartinez about 2 years ago - 4 comments

#1246 - Convert the openff small molecule topology to gromacs topology

Issue - State: closed - Opened by xiki-tempula about 2 years ago - 1 comment

#1245 - Save the dihedral section that is not present in the original topology

Issue - State: closed - Opened by xiki-tempula about 2 years ago - 3 comments

#1244 - OpenMM Topology to ParmEd error: 'Topology' object has no attribute 'chains'

Issue - State: closed - Opened by micaela-matta about 2 years ago - 2 comments

#1243 - SMIRNOFF improper torsions are being incorrectly identified as proper torsions

Issue - State: open - Opened by rosemary-cresset about 2 years ago - 2 comments

#1242 - OpenMM 7.70 compatibility issue

Issue - State: open - Opened by pharmlife over 2 years ago - 2 comments

#1241 - MD

Issue - State: closed - Opened by mlec1 over 2 years ago

#1240 - write PDB conect records for S-S bridges and HETATM

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 2 comments

#1239 - Added 3D-RISM with sander to mdin

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 7 comments

#1238 - Alpha angle is written to prmtop BOX_DIMENSIONS instead of beta

Issue - State: closed - Opened by rosemary-cresset over 2 years ago - 2 comments

#1237 - Atom numbers change after CHARMM->Gromacs conversion for glycoproteins.

Issue - State: open - Opened by fhh2626 over 2 years ago

#1236 - Added CONECT records

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 2 comments

#1235 - Added CONECT records

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 1 comment

#1234 - Fix AmberParm.from_structure with CMAPs v3.4

Pull Request - State: closed - Opened by swails over 2 years ago

#1233 - Fix AmberParm.from_structure with CMAPs

Pull Request - State: closed - Opened by swails over 2 years ago

#1232 - Fix energy printout

Pull Request - State: closed - Opened by swails over 2 years ago

#1231 - differences between tleap and parmed when assigning ATOM_TYPE_INDEX

Issue - State: closed - Opened by marioernestovaldes over 2 years ago - 3 comments

#1230 - PBRadii

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 4 comments

#1229 - New pb radii sets for master branch

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 1 comment

#1228 - Amber19SB and cmaps

Issue - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 4 comments

#1227 - New pb radii sets

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago

#1226 - New PBRadii sets

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 2 comments

#1225 - Reading a Gromacs topology fails with insertion code or negative number

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 1 comment

#1224 - Do not force CMAPs to write a ChamberParm instance

Pull Request - State: closed - Opened by swails over 2 years ago

#1223 - Add new PBRadii sets

Issue - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 1 comment

#1222 - Reading a Gromacs topology fails with insertion code or negative number

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 1 comment

#1220 - reading gromacs topologies with insertion codes fixed

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago - 1 comment

#1217 - frame dimension is 0 in AMBER netcdf files written using parmed NETCDFReporter

Issue - State: open - Opened by nrkssa over 2 years ago - 8 comments

#1214 - Bug in the assignment of NBFIXes in Amber topologies

Issue - State: open - Opened by milafternoon over 2 years ago - 3 comments
Labels: bug

#1213 - Weird processing of NBFIXes when using Gromacs topologies for OpenMM

Issue - State: open - Opened by milafternoon over 2 years ago - 4 comments

#1206 - Add fixes to external bond perception for glycans

Pull Request - State: open - Opened by zhang-ivy over 2 years ago - 8 comments

#1199 - Fix issue with colliding atom types in structure addition

Pull Request - State: closed - Opened by swails over 2 years ago - 4 comments

#1183 - Recalculate 1-4 nonbonded terms in combining_rules setter

Pull Request - State: closed - Opened by daico007 almost 3 years ago

#1157 - Add support for more CHARMM force fields

Pull Request - State: closed - Opened by swails over 3 years ago - 2 comments

#1152 - Fix a bug where parm.save() would convert to a ChamberParm if CMAPs were present, even though Amber has CMAPs now

Pull Request - State: closed - Opened by swails over 3 years ago - 2 comments

#1126 - Dependencies?

Issue - State: closed - Opened by emleddin over 3 years ago - 8 comments

#1117 - Error due to mixed 1-4 scaling when converting AMBAR files to the GROMACS format

Issue - State: open - Opened by wehs7661 over 3 years ago - 3 comments

#1101 - How to update LENNARD_JONES parameters after applying a mask ?

Issue - State: open - Opened by theaudebroise almost 4 years ago - 4 comments

#1056 - charmm parameters to openmm

Issue - State: closed - Opened by sawstory about 5 years ago - 1 comment

#1030 - OpenMM to Parmed to Gromacs Errors

Issue - State: closed - Opened by nividic over 5 years ago - 6 comments
Labels: enhancement

#1029 - Mol2 parser error with multiple residues

Issue - State: open - Opened by austinjpaul over 5 years ago - 5 comments

#992 - Error - parmed.exceptions.GromacsError: Structure has mixed 1-4 scaling which is not supported by Gromacs

Issue - State: closed - Opened by tarsisferreira about 6 years ago - 3 comments

#992 - Error - parmed.exceptions.GromacsError: Structure has mixed 1-4 scaling which is not supported by Gromacs

Issue - State: closed - Opened by tarsisferreira about 6 years ago - 3 comments

#834 - Fix unicode encode/decoding in .top comment

Pull Request - State: closed - Opened by ctk3b over 7 years ago - 12 comments

#826 - write CONECT record?

Issue - State: open - Opened by hainm over 7 years ago - 18 comments

#647 - Error during conversion from gromacs topology to amber topology

Issue - State: closed - Opened by rahmanhpu over 8 years ago - 5 comments

#543 - Correct Gromacs func # for RB torsions

Pull Request - State: closed - Opened by ctk3b over 8 years ago

#541 - Respect `parametrize` flag when reading .top files

Pull Request - State: closed - Opened by ctk3b over 8 years ago - 7 comments

#305 - Write CHARMM parameter files and PSFs

Issue - State: closed - Opened by swails almost 9 years ago - 19 comments
Labels: enhancement, Major

GitHub / ParmEd/ParmEd issues and pull requests