It is very strange to have so much special character for the
"restraintmask" keyword;
the definition of restraintmask would be,
> restraintmask=':1-486',
Jing
On Thu, Jan 5, 2017 at 10:14 AM, 吴萌 <wumeng.shanghaitech.edu.cn> wrote:
> Hi,
> I have followed http://archive.ambermd.org/201603/0160.html to use
> cpptraj to convert the .rst, but the last step 'trajout ###.pdb' kept in
> 'Writing ### as PDB' state and reported without any errors. Actually, it is
> my first time to use amber to simulate membrane protein, so besides the
> above problem, I have two more questions that confused me so much, Q1: In
> my knowledge, the membrane proteins simulate with the charmm force field
> commonly, I am not sure whether the amber force field is suitable for
> membrane proteins or not, and need I add the charmm force field to amber?
> If I need, how to do it? Q2: Go back to the original problem, I put
> restraints on protein and POPC molecules at the same time in 'Heat.in',
>
> > restraint_wt=10.0
> > restraintmask=':1-486 & !.H=',
>
> is it acceptable to do so? My thought is to restrain the protein and
> membrane in the whole heating process(NVT), and then release it by
> decreasing restraints in the early period of the production MD
> process(NPT), so if this practice is right or not for the membrane protein?
> Any suggestions would be greatly appreciated. Thank You Very Much!
>
> Sincerely,
> Wu Meng
>
> ###########################################################
> Message: 21
> Date: Wed, 4 Jan 2017 17:13:16 +0200
> From: Huang Jing <jing.huang8911.gmail.com>
> Subject: Re: [AMBER] Problems about membrane protein simulation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAMvERa=tBi4OQN8rDWcULrV6qGXvB1OD+Bn8BCb_73y_wLHD7A.mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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'?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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
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Received on Thu Jan 05 2017 - 02:00:02 PST
