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 - 12:13:29 CST

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 |
>>>>
>>>> Note: Electronic Mail is not secure, has no guarantee of delivery,
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> issues.
>>>>
>>>>
>>>>
>>>>
>>>>
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