[AMBER] Problems about membrane protein simulation

From: Shanghaitech University WuMeng <wumeng.shanghaitech.edu.cn>
Date: Wed, 4 Jan 2017 22:44:22 +0800

Dear All,
  I am working on a membrane protein simulation. I have referred to "An Amber Lipid Force Field Tutorial:Lipid14 Edition"(http://ambermd.org/tutorials/advanced/tutorial16/), the first 'minimization' for my system I run is OK, and the next 'Heating' also run successfully, but when I open 'Heat.rst' in VMD, nothing displayed in the VMD window, then I tried to use ambpdb to transform '.rst' to '.pdb'úČthere came an error:'Could not read restart atoms/time'.(min.rst is OK).It seems there are some mistakes in the 'Heat.rst', here is the 'Heat.in':
####################
Heating 100K
 &cntrl
  imin=0,
  ntx=1,
  irest=0,
  ntc=2,
  ntf=2,
  tol=0.0000001,
  nstlim=2500,
  ntt=3,
  gamma_ln=1.0,
  ntr=1,
  ig=-1,
  ntpr=100,
  ntwr=10000,
  ntwx=100,
  dt=0.002,
  nmropt=1,
  ntb=1,
  ntp=0,
  cut=10.0,
  ioutfm=1,
  ntxo=2,
  restraint_wt=10.0
  restraintmask=':1-486 & !.H=',
 /
 &wt
  type='TEMP0',
  istep1=0,
  istep2=2500,
  value1=0.0,
  value2=100.0 /
 &wt type='END' /
######################
I add restraints on protein and POPC molecules(RES 1-486), I don't know if it is right or not, this is the first time I use amber to simulate membrane protein, so maybe somewhere I missed or did in the wrong way. Any suggestions or reference resources about membrane protein simulation would be greatly appreciated. Thank You Very Much!


Sincerely,
Wu Meng
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Received on Wed Jan 04 2017 - 07:00:03 PST
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