Re: [AMBER] Problems about membrane protein simulation

From: <wumeng.shanghaitech.edu.cn>
Date: Thu, 5 Jan 2017 08:14:51 +0000

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 05 2017 - 00:30:03 PST
Custom Search