AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Nov 04 2008 - 11:53:48 CST

(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, may not
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>> read every day, and should not be used for urgent or sensitive issues.
>>
>>
>>
>>
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