Dear All,
Suppose I have 1 chain protein with residue from 1 to 119, the restraintmask is as following.
restraintmask = ':1-119 & !.H=',
But if I have a protein complex, 1 chain with residue from 1 to 119, the other chain with residue from 1 to 30, will you please tell me the restraintmask?
If I have a protiein-ligand complex, then how can I define the restraintmask?
I am looking forward to getting your reply.
Cheers,
Acoot
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
To: Acoot Brett <acootbrett.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 9 April 2012 8:43 AM
Subject: Re: [AMBER] the command to make the sander running visible
what do you mean 'it does not run'
AFTER you type the command with the &, you should get a unix prompt
back, right ?
type ps and you should see the process running
On 4/8/12 6:29 PM, Acoot Brett wrote:
> Dear Adrian,
>
> Without "&" at the end, the command runs. With"&" at the end, the command does not run at all.
>
> I dot not know what is the problem
>
> Cheers,
>
> Acoot
>
>
> ________________________________
> From: Adrian Roitberg<roitberg.ufl.edu>
> To: AMBER Mailing List<amber.ambermd.org>
> Sent: Monday, 9 April 2012 12:37 AM
> Subject: Re: [AMBER] the command to make the sander running visible
>
> if you really typed
>
> $AMBERHOME/exe/sander -O -i polyAT_vac_md1_12Acut.in -o
> polyAT_vac_md1_12Acut.out -c polyAT_vac_init_min.rst -p polyAT_vac.prmtop
> -r polyAT_vac_md1_12Acut.rst -x polyAT_vac_md1_12Acut.mdcrd tail -f
> polyAT_vac_md1_12Acut.out
>
> then indeed, it is wrong.
>
> everything after sander is READ by sander itself
>
> tail is not something sander understands
>
>
> Assuming you are running this interactively in your machine, then try
>
> $AMBERHOME/exe/sander -O -i polyAT_vac_md1_12Acut.in -o
> polyAT_vac_md1_12Acut.out -c polyAT_vac_init_min.rst -p polyAT_vac.prmtop
> -r polyAT_vac_md1_12Acut.rst -x polyAT_vac_md1_12Acut.mdcrd&
>
> note the& at the end
>
> this sends it to background.
>
> THEN you can type
>
> tail -f polyAT_vac_md1_12Acut.out
>
>
>
>
> On 4/8/12 10:28 AM, Aron Broom wrote:
>> I'm not sure, but I suspect you can get it working by doing something like
>> -o stdout
>>
>> Then instead of sending the output to the file, it will just print it on
>> the screen. If you want both, I'm sure there is a way to get that to
>> happen, but I'm not sure these are AMBER specific questions (at least in
>> the way I'm answering it), but more linux shell questions.
>>
>> ~Aron
>>
>> On Sun, Apr 8, 2012 at 9:10 AM, Acoot Brett<acootbrett.yahoo.com> wrote:
>>
>>> Dear All,
>>>
>>> I have tried to use tail, but it does not work
>>>
>>> I use the following command, is anything wrong?
>>> "$AMBERHOME/exe/sander -O -i polyAT_vac_md1_12Acut.in -o
>>> polyAT_vac_md1_12Acut.out -c polyAT_vac_init_min.rst -p polyAT_vac.prmtop
>>> -r polyAT_vac_md1_12Acut.rst -x polyAT_vac_md1_12Acut.mdcrd tail -f
>>> polyAT_vac_md1_12Acut.out"
>>>
>>> It says tail cannot be recognized.
>>>
>>> I am looking forward to getting your reply on how to solve the problem.
>>>
>>> Cheers,
>>>
>>> Acoot
>>>
>>>
>>> ----- Original Message -----
>>> From: Acoot Brett<acootbrett.yahoo.com>
>>> To: AMBER Mailing List<amber.ambermd.org>
>>> Cc:
>>> Sent: Sunday, 8 April 2012 10:13 PM
>>> Subject: [AMBER] the command to make the sander running visible
>>>
>>> Dear All,
>>>
>>> As for the sander MD step usually takes a long time, it makes the computer
>>> looks like dead.
>>>
>>> Will you please tell me the sander command to show the sander MD process
>>> is on going, especially the sander command which indicates how much time
>>> left to complete the on-going sander step?
>>>
>>> Cheers,
>>>
>>> Acoot
>>>
>>> _______________________________________________
>>> 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
>>>
>>
>>
>>
>
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Sun Apr 08 2012 - 19:30:03 PDT
