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
----- 禄脴赂麓脫脢录镁 -----
路垄脨脜脠脣:David A Case <case.biomaps.rutgers.edu>
脢脮脨脜脠脣:录脥脧镁路氓 <jixf.ysfri.ac.cn>,AMBER Mailing List <amber.ambermd.org>
脢卤 录盲:2013脛锚03脭脗15脠脮 19脢卤48路脰
脰梅 脤芒:Re: [AMBER] the protein was crashed
On Fri, Mar 15, 2013, 录脥脧镁路氓 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 25 2013 - 20:00:03 PDT
