Amber-MD cpptraj issues

Amber-MD / cpptraj

Biomolecular simulation trajectory/data analysis.

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issues

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Implement ability to calculate vector magnitude in 'vectormath' command.

#1105 drroe closed 3 days ago
0
Export dataset based on maths and distances

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

#1103 mkgilson opened 3 weeks ago
1
Attempt to fix pytraj test.

#1102 drroe closed 4 weeks ago
3
Add 'rescut' and 'bondoffset' keywords to 'prepareforleap'

#1101 drroe closed 1 month ago
0
Minor fix for PSF with NUMLP

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

#1099 drroe closed 1 month ago
5
Test compatibility with Drude trajectories

#1098 drroe closed 1 month ago
4
Should multidihedral allow pseudo dihedrals?

#1097 drroe opened 1 month ago
0
Average structure not being distributed to all ranks in parallel

#1096 drroe opened 2 months ago
0
Creating mass-weighted covariance matrix

#1095 fatih4534 opened 2 months ago
2
Update CUDA support

#1094 drroe closed 2 months ago
0
Fix compilation on ARM based systems

#1093 drroe closed 2 months ago
1
Add 'addatom' action

#1092 drroe closed 2 months ago
1
Fix which atoms are reported in DSSP "missing atoms" warning message

#1091 drroe closed 3 months ago
1
Res TYR:1063 is missing atoms N

#1090 H-EKE closed 3 months ago
4
vector definition

#1089 H-EKE closed 2 months ago
5
Handle blank lines at the end of Karplus data file for jcoupling action

#1088 drroe closed 3 months ago
5
clang 15.0.7: testp.cpp:2:14: error: use of undeclared identifier 'printf'

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

#1086 drroe closed 3 months ago
1
Add --disable-nczarr flag to netcdf configure

#1085 drroe closed 4 months ago
1
lDDT measure

#1084 rodrigogalindo opened 4 months ago
0
Error: No reference atoms selected for parm , [@CA]

#1083 H-EKE closed 2 months ago
16
Fix ambpdb build

#1082 drroe closed 4 months ago
0
Fix detection of NAMD-style unit cell parameters for NAMD DCD

#1081 drroe closed 4 months ago
0
Fix automatic identification of CIF files.

#1080 drroe closed 4 months ago
0
Add 'byfac' keyword to change mass/charge command

#1079 drroe closed 5 months ago
0
K-means++ Style initialization

#1078 drroe opened 5 months ago
0
Add ability to offset charge/mass, save charge/mass to variables

#1077 drroe closed 5 months ago
0
Fixes for'atommap'

#1076 drroe closed 5 months ago
0
Add TICA, max/min distance calc, and data projection commands

#1075 drroe closed 5 months ago
0
'atommap' command unexpected result

#1074 juan-alcantara1 closed 5 months ago
8
cpptraj

#1073 H-EKE closed 3 months ago
6
running multiple analysis in single file question

#1072 groponp closed 5 months ago
4
Install cpptraj las version

#1071 groponp closed 5 months ago
10
Problems on ARM systems

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

#1069 hainm closed 7 months ago
8
Do not use "bad" box info from PDB files

#1068 drroe closed 7 months ago
3
Add command line flag to calculate charge

#1067 drroe closed 8 months ago
0
Add ability to extract box information to a data set

#1066 drroe closed 8 months ago
1
Selecting second molecule

#1065 almeida85 closed 5 months ago
3
Improve unit cell detection for charmm trajectory (dcd) files

#1064 drroe closed 8 months ago
0
If wildcard expansion fails in a list for loop, do not add to the loop.

#1063 drroe closed 8 months ago
1
Pin the cython version. Does not appear to work with cython 3.X.X.

#1062 drroe closed 9 months ago
2
Fix the -DDEBUG compile

#1061 drroe closed 9 months ago
2
Add ability to change names in 'atommap' command

#1060 drroe closed 9 months ago
3
Add note about strip and atomicfluct with `pdbres` keyword

#1059 slochower closed 9 months ago
3
Unable to Install pytraj from source code on Linux using cpptraj (Ubuntu 22.04.3 LTS)

#1058 PhiMykah closed 10 months ago
2
Are the options for `parmopts` documented anywhere?

#1057 slochower closed 9 months ago
16
Add 'mergeres' keyword to 'change' command

#1056 drroe closed 10 months ago
0