ffmpeg -i input.mkv -acodec ac3 -ab 640k -ac 6 -vcodec copy output.mkv

ffmpeg version N-32077-g5f5e37e, Copyright (c) 2000-2011 the FFmpeg developers
  built on Aug 24 2011 17:01:01 with gcc 4.4.5
  configuration: --enable-gpl --enable-libfaac --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libtheora --enable-libvorbis --enable-libx264 --enable-libxvid --enable-nonfree --enable-postproc --enable-version3 --enable-x11grab
  libavutil    51. 13. 0 / 51. 13. 0
  libavcodec   53. 12. 0 / 53. 12. 0
  libavformat  53.  9. 0 / 53.  9. 0
  libavdevice  53.  3. 0 / 53.  3. 0
  libavfilter   2. 34. 2 /  2. 34. 2
  libswscale    2.  0. 0 /  2.  0. 0
  libpostproc  51.  2. 0 / 51.  2. 0
[matroska,webm @ 0x14d9c60] max_analyze_duration 5000000 reached at 5000000
[matroska,webm @ 0x14d9c60] Estimating duration from bitrate, this may be inaccurate

Seems stream 0 codec frame rate differs from container frame rate: 1073741824.00 (1073741824/1) -> 23.98 (24000/1001)
Input #0, matroska,webm, from 'input.mkv':
  Duration: 01:29:51.30, start: 0.000000, bitrate: 1536 kb/s
    Chapter #0.0: start 0.000000, end 195.946000
    Metadata:
      title           : 00:00:00.000
    Chapter #0.1: start 195.946000, end 326.451000
    Metadata:
      title           : 00:03:15.946
    Chapter #0.2: start 326.451000, end 656.656000
    Metadata:
      title           : 00:05:26.451
    Chapter #0.3: start 656.656000, end 884.550000
    Metadata:
      title           : 00:10:56.656
    Chapter #0.4: start 884.550000, end 1196.904000
    Metadata:
      title           : 00:14:44.550
    Chapter #0.5: start 1196.904000, end 1473.055000
    Metadata:
      title           : 00:19:56.904
    Chapter #0.6: start 1473.055000, end 1894.392000
    Metadata:
      title           : 00:24:33.055
    Chapter #0.7: start 1894.392000, end 2178.510000
    Metadata:
      title           : 00:31:34.392
    Chapter #0.8: start 2178.510000, end 2391.681000
    Metadata:
      title           : 00:36:18.510
    Chapter #0.9: start 2391.681000, end 2632.046000
    Metadata:
      title           : 00:39:51.681
    Chapter #0.10: start 2632.046000, end 2923.045000
    Metadata:
      title           : 00:43:52.046
    Chapter #0.11: start 2923.045000, end 3419.583000
    Metadata:
      title           : 00:48:43.045
    Chapter #0.12: start 3419.583000, end 3701.031000
    Metadata:
      title           : 00:56:59.583
    Chapter #0.13: start 3701.031000, end 4003.124000
    Metadata:
      title           : 01:01:41.031
    Chapter #0.14: start 4003.124000, end 4238.693000
    Metadata:
      title           : 01:06:43.124
    Chapter #0.15: start 4238.693000, end 4570.274000
    Metadata:
      title           : 01:10:38.693
    Chapter #0.16: start 4570.274000, end 4833.871000
    Metadata:
      title           : 01:16:10.274
    Chapter #0.17: start 4833.871000, end 5035.280000
    Metadata:
      title           : 01:20:33.871
    Chapter #0.18: start 5035.280000, end 5221.341000
    Metadata:
      title           : 01:23:55.280
    Chapter #0.19: start 5221.341000, end 5391.307000
    Metadata:
      title           : 01:27:01.341
    Stream #0.0(eng): Video: h264 (High), yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], 23.98 tbr, 1k tbn, 1073741824 tbc (default)
    Stream #0.1(eng): Audio: dts (DTS), 48000 Hz, 5.1, s16, 1536 kb/s (default)
    Stream #0.2(eng): Subtitle: text (default)
    Stream #0.3(cze): Subtitle: text
    Stream #0.4(por): Subtitle: text
    Stream #0.5(nor): Subtitle: text
    Stream #0.6(rum): Subtitle: text
    Stream #0.7(spa): Subtitle: text
File 'output.mkv' already exists. Overwrite ? [y/N] y
Incompatible sample format 's16' for codec 'ac3', auto-selecting format 'flt'
[ac3 @ 0x15ec600] channel_layout not specified
[ac3 @ 0x15ec600] No channel layout specified. The encoder will guess the layout, but it might be incorrect.
Output #0, matroska, to 'output.mkv':
    Stream #0.0(eng): Video: h264, yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], q=2-31, 90k tbn, 1k tbc (default)
    Stream #0.1(eng): Audio: ac3, 48000 Hz, 5.1, flt, 640 kb/s (default)
    Stream #0.2(eng): Subtitle: ssa (default)
Stream mapping:
  Stream #0.0 -> #0.0: copy
  Stream #0.1 -> #0.1: dca -> ac3
  Stream #0.2 -> #0.2: ? -> ass
Decoder (codec text) not found for input stream #0.2