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'，there 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
