AMBER Archive (2008)

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

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Wed Nov 05 2008 - 11:22:33 CST

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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