Re: [AMBER] the protein was crashed

From: <jixf.ysfri.ac.cn>
Date: Tue, 26 Mar 2013 10:24:25 +0800 (CST)

   Dear David,
   thank you very much for your help. I have tried to use the command of
   "autoimage", but the result was the same as before.
   I checked the structure generated in the whole steps, found that after
   "minimize" the protein was crashed. Maybe there were error in the
   preparation of the .prmtop and .inpcrd file.
   the characters were used as this:
   1.solvate the protein in the water:
    source leaprc.ff03.r1
   mol=loadpdb lipase.pdb
   bond mol.54.SG mol.333.SG
   bond mol.68.SG nol.72.SG
   bond mol.153.SG mol.156.SG
   bond mol.298.SG mol.306.SG
   check mol
   solvatebox mol TIP3PBOX 10.0
   saveamberparm mol lipase.prmtop lipase.inpcrd
   quit
   2.delect the water around the lid and solvate the lipase_water in the
   toluene
   source leaprc.gaff
   source leaprc.ff99SB
   source leaprc.ff03.r1
   loadamberparams toluene.frcmod
   loadoff toluene.lib
   lip=loadpdb lipase_water_delH.pdb
   bond lip.153.SG lip.156.SG
   charge lip
   check lip
   TOLBOX=loadpdb toluenebox.pdb
   set TOLBOX restype solvent
   solvatebox lip TOLBOX 12.0
   setBox lip centers
   addions lip Na+ 10
   saveamberparm lip lip.prmtop lip.inpcrd
   quit
   3. and then minimize in restrain
   &cntrl
   imin = 1,
   maxcyc = 5000,
   ncyc = 2500,
   ntb = 1,
   ntr=1,
   !igb = 0,
   drms = 0.1,
   cut = 16.0
   /
   hold the protein fixed
   500
   RES 1 371
   END
   END
   4.minimize without restrain
   &cntrl
   imin = 1,
   maxcyc = 5000,
   ncyc = 2500,
   ntb = 1, ntr=0,
   !igb = 0, ! no periodic box
   drms = 0.1,
   cut = 12.0
   /
   please help me ,what has happened?
   Thanks!
   xiaofeng

   ----- »Ø¸´Óʼþ -----
   ·¢ÐÅÈË:David A Case <case.biomaps.rutgers.edu>
   ÊÕÐÅÈË:¼ÍÏþ·å <jixf.ysfri.ac.cn>,AMBER Mailing List <amber.ambermd.org>
   Ê± ¼ä:2013Äê03ÔÂ15ÈÕ 19ʱ48·Ö
   Ö÷ Ìâ:Re: [AMBER] the protein was crashed

     On Fri, Mar 15, 2013, ¼ÍÏþ·å wrote:
>
> the results showed that the lipase was crashed, it looks like a pile of
> amino acid.
     This looks like it might be an imaging problem. Try running the trajectory
     through cpptraj, using the "autoimage" command.
     ...dac
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Received on Mon Mar 25 2013 - 20:00:03 PDT
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