Re: [AMBER] Problems about membrane protein simulation

From: Huang Jing <jing.huang8911.gmail.com>
Date: Wed, 4 Jan 2017 17:13:16 +0200

http://archive.ambermd.org/201603/0160.html
this mail could be useful to solve your problem;

Jing

On Wed, Jan 4, 2017 at 4:44 PM, Shanghaitech University WuMeng <
wumeng.shanghaitech.edu.cn> wrote:

> 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'´╝îthere 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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>
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Received on Wed Jan 04 2017 - 07:30:02 PST
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