AMBER Archive (2008)

Subject: Re: AMBER: problem with group input and NMR restaints

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Nov 05 2008 - 14:39:29 CST

ok then just for the sake of the archives let's clarify that this
problem has been solved.

On Wed, Nov 5, 2008 at 3:00 PM, priya priya <priyaanand_27_at_yahoo.co.in> wrote:
> Sir,
>
> Thanks for the suggestions and time.
>
> I already had a look into the output file(fib_restwt.out), and It is reading
> the both the restraints, and I have also changed the &wt Type.
>
> Regards
> Priya
>
>
>
> --- On Wed, 5/11/08, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
>
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> Subject: Re: AMBER: problem with group input and NMR restaints
> To: amber_at_scripps.edu
> Date: Wednesday, 5 November, 2008, 11:43 PM
>
> the file fib_restwt.out shows that sander read and understood the
> restraint mask, and applied it to 1434 atoms.
> it also read 1 restraint from your disang file.
>
> so- I don't see a problem. can you clarify what you think is going wrong?
>
> also, there is no need to put REST in the weight change section, since
> you
> are not changing it.
>
>
> On Wed, Nov 5, 2008 at 12:22 PM, priya priya <priyaanand_27_at_yahoo.co.in>
> wrote:
>>
>> Plz find the attachments
>> --- On Wed, 5/11/08, Carlos Simmerling <carlos.simmerling_at_gmail.com>
> wrote:
>>
>> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>> Subject: Re: AMBER: problem with group input and NMR restaints
>> To: amber_at_scripps.edu
>> Date: Wednesday, 5 November, 2008, 10:23 PM
>>
>> I did not receive attachments
>>
>>
>>
>> On Wed, Nov 5, 2008 at 11:05 AM, priya priya
> <priyaanand_27_at_yahoo.co.in>
>> wrote:
>>> HI
>>>
>>> Attaching the 2 output files:
>>> 1) fib_group.out : In which the group has been moved to the last. It
> shows
>>> some error.
>>> 2) fib_restwt.out: In which i applied the restraint mask.
>>>
>>>
> Secondly,
>>>
>>> &wt type= 'REST', istep1
>> =0, istep2=0, value1=1.0,
>> value2=1.0, /
>>>
>>> This line was to represent that REST to be from step 1 to the end with
>> value
>>> remaining the same and the keyword was used "REST", for the
>> distance rest,
>>> If i am not wrong.
>>>
>>> I am also trying with: &wt TYPE =END
>>>
>>> Stage 1
>>> &cntrl
>>> imin=0, irest=0, ntx=1,
>>> nstlim=100000, dt=0.002,gbsa =1,surften=0.005,
>>> ntc=2, ntf=2,ntr=1,
>>> ntt=3, gamma_ln =5.0,
>>> tempi=0.000, temp0=300.19,
>>> ntpr=500, ntwx=500, ntwr = 500,
>>> ntb=0, igb=1,nmropt=1,
>>> cut=16,
>>> restraint_wt=1.0,
>>> restraintmask=':1-100'
>>> /
>>>
>>> &wt
>>>
>>>
> TYPE="END",
>>> &end
>>>
>>> DISANG=rst
>>>
>>> /
>>>
>>> There is an option &wt TYPE = END, but i dont know that would
> work.
>>>
>>>
>> Regards
>>> Priya
>>>
>>>
>>>
>>> --- On Tue, 4/11/08, Carlos Simmerling
> <carlos.simmerling_at_gmail.com>
>> wrote:
>>>
>>> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>>> Subject: Re: AMBER: problem with group input and NMR restaints
>>> To: amber_at_scripps.edu
>>> Date: Tuesday, 4 November, 2008, 11:23 PM
>>>
>>> (1)
>>> I'll try to make it more clear-
>>> in your sander input, you have in the &wt section a line that
>>> specifies the "REST" variable.
>>>
>>> here is the line:
>>>
>>> &wt type= 'REST', istep1 =0, istep2=0,
> value1=1.0,
>> value2=1.0, /
>>>
>>> why do you do this?
>>>
>>> (2)
>>> the sander output is for the one with the group input in the wrong
>>> location. what is the sander output when you do either of the things
>>> I
>>> suggested, such as moving the group input to the end, or using
>>>
>> restraintmask?
>>>
>>>
>>>
>>> On Tue, Nov 4, 2008 at 12:38 PM, priya priya
>> <priyaanand_27_at_yahoo.co.in>
>>> wrote:
>>>> Hi ,
>>>>
>>>> I am attaching the sander output file created.
>>>>
>>>> "why are you changing REST in the weight change?", Sorry
> I
>>> couldn;t get what
>>>> you are asking about.
>>>>
>>>> Regards
>>>>
>>>>
>>>> --- On Tue, 4/11/08, Carlos Simmerling
>>
> <carlos.simmerling_at_gmail.com>
>>> wrote:
>>>>
>>>> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>>>> Subject: Re: AMBER: problem with group input and NMR restaints
>>>> To: amber_at_scripps.edu
>>>> Date: Tuesday, 4 November, 2008, 10:11 PM
>>>>
>>>> I think you need to start sending us the sander output so we can
> see
>>>> what sander is doing.
>>>>
>> also-
>>>>
>>>>
>>>>
>>>> On Tue, Nov 4, 2008 at 11:16 AM, priya
>>> priya
>>> <priyaanand_27_at_yahoo.co.in>
>>>> wrote:
>>>>> Hi,
>>>>>
>>>>> I have tried with this
>>>> input file also, but it is not reading the group
>>>>> file.
>>>>> Is there any other way to do this.
>>>>>
>>>>> Another
> option i tried is :
>>>>> Stage 1
>>>>> &cntrl
>>>>> imin=0, irest=0, ntx=1,
>>>>> nstlim=100000, dt=0.002,gbsa =1,surften=0.005,
>>>>> ntc=2, ntf=2,ntr=1,
>>>>> ntt=3, gamma_ln =5.0,
>>>>> tempi=0.000, temp0=300.19,
>>>>> ntpr=500, ntwx=500, ntwr = 500,
>>>>> ntb=0, igb=1,nmropt=1,
>>>>> cut=16,
>>>>> restraint_wt=1.0,
>>>>> restraintmask=':1-100'
>>>>> /
>>>>> &wt type=
>> 'REST', istep1 =0, istep2=0, value1=1.0,
>>>> value2=1.0, /
>>>>> &wt type='END' /
>>>>> DISANG=rst
>>>>> END
>>>>>
>>>>>
>>>>> Will this
>>> restraint_wt=1.0,
>>>>> restraintmask=':1-100' do the same thing as
> the
> group
>> do.
>>>>>
>>>>> Regards
>>>>> priya
>>>>>
>>>>> --- On Tue, 4/11/08, Ross Walker <ross_at_rosswalker.co.uk>
>> wrote:
>>>>>
>>>>> From: Ross Walker
>>>> <ross_at_rosswalker.co.uk>
>>>>> Subject: RE: AMBER: problem with group input and NMR restaints
>>>>> To: amber_at_scripps.edu
>>>>> Date: Tuesday, 4 November, 2008, 9:16 PM
>>>>>
>>>>> Hi Priya,
>>>>>
>>>>> I'm not sure if you can use NMR restraints with harmonic
>>> restraints, I
>>>> have
>>>>> never tried it although I
>> don't see why it wouldn't work.
>> With
>>>> regards
>>>>> to your input I think the group input has to come last. so
> your
>> input
>>>>
> should
>>>>> probably be:
>>>>>
>>>>> Stage 1
>>>>> &cntrl
>>>>> imin=0, irest=0, ntx=1,
>>>>> nstlim=100000,
>>> dt=0.002,gbsa =1,surften=0.005,
>>>>> ntc=2, ntf=2,ntr=1,
>>>>> ntt=3, gamma_ln =5.0,
>>>>> tempi=0.000, temp0=300.19,
>>>>> ntpr=500, ntwx=500, ntwr =
>>>>> 500,
>>>>> ntb=0, igb=1,nmropt=1,
>>>>> cut=16
>>>>> /
>>>>> &wt type= 'REST', istep1 =0, istep2=0,
> value1=1.0,
>>>> value2=1.0, /
>>>>> &wt type='END' /
>>>>>
>>>> DISANG=rst
>>>>> END
>>>>> hold the protein fixed
>>>>> 10.0
>>>>> ATOM 1 900
>>>>>
>> END
>>>>>
> END
>>>>>
>>>>> Although you may have to experiment here to be sure.
>>>>>
>>>>> Good luck,
>>>>> Ross
>>>>>
>>>>>
>>>>> /\
>>>>> \/
>>>>> |\oss Walker
>>>>>
>>>>> | Assistant Research Professor |
>>>>> | San Diego Supercomputer Center |
>>>>> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
>>>>> |
>>> http://www.rosswalker.co.uk | PGP Key available on request |
>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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