Amber-MD cpptraj issues

Amber-MD / cpptraj

Biomolecular simulation trajectory/data analysis.

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issues

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Add error message to 'for inmask' when no topology is present

#1116 drroe closed 20 hours ago
0
Calculate states between several probes and a receptor

#1115 H-EKE closed 2 days ago
6
Allow atommap rmsfit to proceed with partial atom maps

#1114 drroe opened 3 weeks ago
0
Fix parallel handling of data in repeated trajectory runs for 'rotate' and 'average'

#1113 drroe closed 3 weeks ago
0
Fix handling of generated rotation matrix sets in parallel with the 'rotate' command

#1112 drroe closed 4 weeks ago
0
Improve atom mapping between chiral centers

#1111 drroe closed 1 month ago
0
Doing a new release?

#1110 xiki-tempula opened 1 month ago
0
Add energy decomposition (with PME)

#1109 drroe closed 1 month ago
0
Multidihedral pca -> sidechain pca?

#1108 H-EKE opened 1 month ago
0
Cumulative radial distribution function

#1107 Saqlain5565 opened 1 month ago
0
Can CPPTRAJ read the dat file which is produced by other tool?

#1106 MilesYyh closed 1 month ago
5
Implement ability to calculate vector magnitude in 'vectormath' command.

#1105 drroe closed 1 month ago
0
Export dataset based on maths and distances

#1104 H-EKE closed 1 month ago
2
Puzzled by atom-based masking of energies

#1103 mkgilson closed 3 weeks ago
2
Attempt to fix pytraj test.

#1102 drroe closed 2 months ago
3
Add 'rescut' and 'bondoffset' keywords to 'prepareforleap'

#1101 drroe closed 2 months ago
0
Minor fix for PSF with NUMLP

#1100 drroe closed 3 months ago
1
Recognize Drude particles, improve handling of lone pairs

#1099 drroe closed 3 months ago
5
Test compatibility with Drude trajectories

#1098 drroe closed 2 months ago
4
Should multidihedral allow pseudo dihedrals?

#1097 drroe opened 3 months ago
0
Average structure not being distributed to all ranks in parallel

#1096 drroe closed 3 weeks ago
1
Creating mass-weighted covariance matrix

#1095 fatih4534 opened 4 months ago
3
Update CUDA support

#1094 drroe closed 4 months ago
0
Fix compilation on ARM based systems

#1093 drroe closed 4 months ago
1
Add 'addatom' action

#1092 drroe closed 4 months ago
1
Fix which atoms are reported in DSSP "missing atoms" warning message

#1091 drroe closed 4 months ago
1
Res TYR:1063 is missing atoms N

#1090 H-EKE closed 4 months ago
4
vector definition

#1089 H-EKE closed 4 months ago
5
Handle blank lines at the end of Karplus data file for jcoupling action

#1088 drroe closed 5 months ago
5
clang 15.0.7: testp.cpp:2:14: error: use of undeclared identifier 'printf'

#1087 hainm closed 5 months ago
3
CIF fixes, preserve CHARMM PSF segment ID

#1086 drroe closed 5 months ago
1
Add --disable-nczarr flag to netcdf configure

#1085 drroe closed 6 months ago
1
lDDT measure

#1084 rodrigogalindo opened 6 months ago
0
Error: No reference atoms selected for parm , [@CA]

#1083 H-EKE closed 4 months ago
16
Fix ambpdb build

#1082 drroe closed 6 months ago
0
Fix detection of NAMD-style unit cell parameters for NAMD DCD

#1081 drroe closed 6 months ago
0
Fix automatic identification of CIF files.

#1080 drroe closed 6 months ago
0
Add 'byfac' keyword to change mass/charge command

#1079 drroe closed 6 months ago
0
K-means++ Style initialization

#1078 drroe opened 7 months ago
0
Add ability to offset charge/mass, save charge/mass to variables

#1077 drroe closed 7 months ago
0
Fixes for'atommap'

#1076 drroe closed 7 months ago
0
Add TICA, max/min distance calc, and data projection commands

#1075 drroe closed 7 months ago
0
'atommap' command unexpected result

#1074 juan-alcantara1 closed 7 months ago
8
cpptraj

#1073 H-EKE closed 5 months ago
6
running multiple analysis in single file question

#1072 groponp closed 7 months ago
4
Install cpptraj las version

#1071 groponp closed 7 months ago
10
Problems on ARM systems

#1070 drroe closed 4 months ago
2
WIP - Playing with conda env for now (DO NOT MERGE)

#1069 hainm closed 8 months ago
8
Do not use "bad" box info from PDB files

#1068 drroe closed 8 months ago
3
Add command line flag to calculate charge

#1067 drroe closed 9 months ago
0