AMBER Archive (2008)

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

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Tue Nov 04 2008 - 11:38:37 CST

 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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