Hi,
On Thu, Jan 5, 2017 at 3:14 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.
Do you mean cpptraj was hanging and not writing the PDB? Did it exit
with an error? Were you running interactively and didn't actually type
'run'. Could you provide some more details? Does something like
'cpptraj -p <topology file> -y heat.rst -x heat.pdb' not work? I
suspect your original issue is that the default restart format for
Amber16 is NetCDF which VMD does not yet read (although I think
support is coming soon).
> 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?
See section '3.4 Lipids' in the Amber 16 manual and references
therein, particularly
http://pubs.acs.org/doi/abs/10.1021/ct4010307.
> 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!
That restraintmask looks fine, but 10.0 seems like quite a high force
constant. I would start at no more than 5. Also, you probably want to
gradually reduce the restraint weight in successive runs until you can
eliminate it.
-Dan
>
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Jan 05 2017 - 06:30:02 PST
