AMBER Archive (2008)

Subject: RE: AMBER: stripping water from a restart file

From: CHAMI F. (fatima.chami_at_durham.ac.uk)
Date: Wed Oct 22 2008 - 15:29:45 CDT

 

________________________________

From: owner-amber_at_scripps.edu on behalf of Bill Ross
Sent: Wed 22/10/2008 18:12
To: amber_at_scripps.edu
Subject: Re: AMBER: stripping water from a restart file

> I tried to run an MD simulation of my solute in vacuum but sander =
> failed to read the modified restart file

What error msg was given?

  Unit 30 Error on OPEN: dimer-vac_md.rst_1000000

---------------------------------------

trajectory generated by ptraj
   78
  16.2977970 9.2525572 28.3833405 16.4277889 8.7509776 27.4593768
  15.1185889 9.8859212 28.6764193 14.3042028 9.8067596 27.9421672
  14.9693455 10.5185641 29.9313931 13.3292631 11.0226798 30.4723278
  13.1930395 10.4097674 31.7223311 13.2925901 12.4378535 30.5958041
  12.3512003 10.5815000 29.5641934 15.9917001 10.4095327 30.9166159
  15.9146159 10.7438642 31.9390128 17.1854510 9.9114679 30.5318918
  17.9888966 9.8083049 31.2364514 17.3186338 9.2334478 29.3298609
  18.4888122 8.5960123 28.9121849 18.3112077 7.7804295 28.2917044
  19.7905035 8.8969633 29.1509894 20.8341015 8.5474255 28.4551276
  22.1021730 9.2003141 28.7448755 22.1867797 10.2417925 29.7489314
  23.4097671 10.8653659 29.9851863 24.5247109 10.4344721 29.2387639
  24.4259273 9.4772320 28.2252963 25.3612973 9.2084833 27.6371666
  26.0895781 11.1782276 29.6024028 26.1000604 11.5970975 30.9984176
  27.1325492 10.2409588 29.3318720 26.1417307 12.2995660 28.7078128
  23.4946415 11.5725272 30.8454830 21.3146457 10.5392570 30.3073026
  23.2003698 8.8569283 27.8917593 23.1696757 7.8564319 26.8837538
  24.0373970 7.6024105 26.2992468 21.9161645 7.2694877 26.6007545
  21.8672395 6.5148442 25.8612158 20.6679402 7.5206131 27.3282556
  19.6977059 6.8149563 27.1536903 17.8891347 5.4906990 30.6138545
  18.5904341 4.9617371 29.9299875 16.5281394 5.3595049 30.4488728
  16.0959317 4.7977760 29.6200601 15.6342647 6.0883524 31.2681036
  13.8662494 5.8842265 30.9650410 13.6763713 4.5735572 30.3408248
  13.3549330 5.9894365 32.3625002 13.4779530 7.0207403 30.1824152
  16.1058845 6.9705289 32.2430434 15.3966691 7.5211692 32.9770264
  17.4975206 7.0400203 32.4501882 17.8580097 7.6239161 33.3241550
  18.3803512 6.2623598 31.6643164 19.7470500 6.3492895 31.7034335
  20.3132471 5.9933026 30.9275364 20.4586913 7.2001539 32.4612935
  21.6496750 7.5730845 32.1814021 22.1829761 8.6285086 32.9321707
  21.4231233 9.4120783 33.8273306 22.0079034 10.4694748 34.4872838
  23.3371203 10.8116395 34.3572331 24.1096795 10.0777035 33.4232387
  25.1359195 10.3118911 33.2287937 24.0063664 12.0664117 35.2998604
  23.0347890 13.1365064 35.3104314 24.2357739 11.5215807 36.6171612
  25.1927064 12.4678267 34.6007860 21.3852271 11.0245035 35.2036048
  20.3365247 9.1659640 34.0582489 23.5304407 8.9661459 32.7836303
  24.3654540 8.2519939 31.8128262 25.3635319 8.4726992 31.6529202
  23.8030628 7.3810365 30.9783587 24.4259370 6.9536407 30.1887022
  22.4190313 6.9384752 31.0633215 21.9367543 6.0918241 30.3329877
  22.8433701 59.2471665 10.2871456 -17.0921266 22.1136801 12.3395469
  17.9574027 37.0806085 28.1395414 35.3702838 24.0320276 -12.3655992
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
  47.5548619 48.0586172 47.1058278 90.0000000 90.0000000 90.0000000

------------------------------------------------------------------------------------------------

This is my mdin file for a vacuum simulation:

&cntrl
  imin = 0, irest = 0, ntx = 1,
  ntb = 0,
  igb = 0, ntpr = 3000, ntwx = 2000, ntwprt = 78,
  ntt = 3, gamma_ln = 1.0,
  tempi = 300.0, temp0 = 300.0,
  nstlim =1000000, dt =0.001,
  cut = 12.0,
 /
-------------------------------------------------------------------------------------------------------

The modified restart and topology files were successfully loaded into VMD .

I have 150 restart files (solute + solvent) for which i need to do MD simulation of solute in vacuum....i would appreciate your feedback
 
best wishes
Fatima

Bill
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