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bugfix.24: configure: Automagically apply AT15_Amber11.py when necessary (if Amber 11 exists alongside AmberTools 1.5). Fix OpenMP-related segfaults with TRAJ data sets and in the checkstructure action. Numerous updates and improvements. bugfix.1: Make an scf failure a fatal error for sqm, to minimze wasted computer time on a failed calculation.

If you wish to apply the listed AmberTools updates, run configure again and make sure to re-compile Amber/AmberTools. Low resolution refinement[edit] Use an existing high resolution model (e.g. Fix segfault when using parmstrip on a topology that needs to be used to read in a trajectory file. Re: force field for replica exchange with NAMD From: Sndor Kovcs (skovacs_at_wustl.edu) Date: Thu Oct 28 2010 - 17:47:21 CDT Next message: 俞翔: "Re: force field for replica exchange with NAMD"

Privacy policy About CCP4 wiki Disclaimers Sándor Sándor Á. Fix autoimage centering to box center for general triclinic cells. In some cases, such as where generate_henke_cpp.py tries to generate tables from all the files in a directory, it tries to read ._ files as normal files and dies.

Fix potential segfaults that could occur when processing malformed mask expressions. Usage examples: phenix.reciprocal_space_arrays model.pdb data.hkl f_obs_label="IOBS" phenix.reciprocal_space_arrays model.pdb data.hkl r_free_flags_label="FREE" Output: MTZ file with data arrays. Fix reading of restart files with # atoms > 5 digits. bugfix.15: Fixes issues in ptraj. 1) output of cluster trajectory could cause a segfault when trajectory became too large. 2) Fixes minor bug in secstruct (DSSP) command where turn populations would

update.7: Fixes for paramfit and chamber: Paramfit: Overall, significantly more user friendly Fix bug where Paramfit expects quantum data file when it's not needed Improved parameters to fit file format Can bugfix.18: Ptraj: Several bugfixes. (1) Fix bug in 'closest' where wrong distances calcd if no box info present. (2) Fix minor memory error in 'secstruct'. (3) Correct behavior of 'vector principal' Fix counting of bonds in temperature command (only affects ntc > 1). Fix 'stat' analysis command: torsion values between 0.0 and 30.0 are now correctly assigned as 'c'.

update.8: Fixes a potential issue with the configure script on certain platforms (like Ubuntu) when trying to do a CUDA build. PDB: Residue numbers > 9999 and atom numbers > 99999 now wrap to 0 instead of 1 to make atom/residue counting easier. phenix.pdbtools can also add hydrogens (FIXME: what are the differences?). The example uses > alain.params which is modified from Charmm19 force field.

phenix.reciprocal_space_arrays[edit] computes various arrays such as Fcalc, Fmask, Fmodel, Fbulk, and more. From version 1.0.5 to 1.0.8. Look for the max memory intake in the last record (towards the end of log file). Fix and improve reading of MDOUT files.

I checked namd-l and found out that > some people who used Charmm22 force filed directly also faced the > similar problem that Charmm22 could not be correctly read but none See my post of a few days ago. Any bugfixes that appear to have already been applied will be skipped. Refinement with mmtbx.lockit[edit] From RWGK's posting to phenixbb on Nov 14, 2010: We have a tool for quick real-space refinement that's geared towards making the geometry ideal in the end.

bugfix.27: NAB and MMPBSA.py: Fix reporting of EDISPER in NAB programs (including mmpbsa_py_energy) when inp is 2. Specifically, Cpptraj: Fix OpenMP compilation with certain PGI compilers. Enable writing of velocity information to Netcdf trajectory files via the 'velocity' keyword. Another example, this time for just doing rigid-body refinement (say, for transferring a model to a crystal with slightly different cell parameters): #!/bin/csh -f rm rigid.1.pdb rigid.1.mtz phaser<

In interactive mode, enable autocompletion for commands as well as file names. bugfix.15: Fix segmentation faults of some pbsa tests when building with Intel compilers version 12. A script documenting the following features using a PDB file (with origin-centered coordinates) as a heavy atom cluster template using two different substructure atomtypes (the cluster, and Fe) using a PDB You can patch your AmberTools distribution to include all of the current bug fixes by downloading this file and saving it in your $AMBERHOME directory.

Inputs: File with reflection data (Fobs or Iobs), R-free flags, and optionally HL coefficients. update.24: Fix for pbsa: reset igb flag in addition to ipb so pbsa cannot be turned on in sander when no charge or radius is read in. PHENIX developers have been working closely with Axel Brunger and Gunnar Schroder to implement DEN in Phenix. bugfix.21: Cpptraj: Fix bug where reading restart files with velocity info after an initial restart with no velocity info would result in corruption of box coordinates.

On Oct 28, 2010, at 3:40 PM, 俞翔 wrote: > Hi Jim, > > I tested replica exchange with Charmm27 force field. bugfix.6: Fixes a number of small bugs for rism1d that were primarily seen on 32-bit operating systems. Instead, it creates a ._ file for each extracted file. NCS usage[edit] phenix.find_ncs - identification of NCS operators[edit] from protein coordinates (chains), heavy atom coordinates, or a density map.

Fix error compiling with old GNU compilers: "DihedralSearch.cpp:53: error: unknown escape sequence '\*'" update.13: Fix ParmEd's NetCDF restart file writing so that netCDF4-Python will create restart files that Amber programs can advanced usage[edit] phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp \ simulated_annealing=true optimize_xyz_weight=true optimize_adp_weight=true main.number_of_macro_cycles=5 \ ordered_solvent=True This will do the following: Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius); bugfix.19: Fix case where even valid options for inp are flagged as illegal choices in MMPBSA.py bugfix.20: Don't mix the ildn and ff99SBnmr fixes, so that leaprc.ff99SBnmr matches the original paper. bugfix.1: Enhancements and fixes for cpptraj.

It is unclear how useful they would be at relatively high resolution (say 2.5A or higher), as there are other restraint methods that work well at that resolution range that are Fix segfault when calculating correlation function for periodic (i.e. You should verify the assignments yourself, however, as it occasionally runs adjacent helices together. Future updates will improve GTX980 performance substantially.

bugfix.27: MMPBSA.py: Fix parsing of Normal Mode entropy output bugfix.28: MMPBSA.py: Fix calculation of standard deviations for normal mode entropy calculations. Version 1.4 1.4 April, 2010 (git tag: v_11) bugfix.all: