AMBER Archive (2006)

Subject: Re: AMBER: MD with positional and NMR restraints

From: David A. Case (case_at_scripps.edu)
Date: Thu Dec 07 2006 - 15:51:53 CST

On Thu, Dec 07, 2006, Mike Summers wrote:

>
> Is there any way to use both positional and NOE restraints? The script
> shown in (C) below runs but does not implement the NOE restraints.
>
>
> (C) (Doesn't apply the NMR restraints.. permutations I've tried also don't work) ############
>
> &cntrl
> nmropt=1,
> imin=0,
> irest=0,
> ntx=1,
> ntb=0,
> cut=10,
> ntc=2,
> ntf=2,
> tempi=0.0,
> temp0=300.0,
> ntt=3,
> gamma_ln=1.0,
> nstlim=10000, dt=0.002,
> ntpr=100, ntwx=100, ntwr=1000
> ntr=1,
> /
>
> &wt type='END' /
> keep main chain atoms frozen
> 500.0
> FIND
> * * M *
> SEARCH
> RES 20 145
> END
> END
>
> &wt type='END' /
> LISTOUT=POUT
> DISANG=../RST.dist
> /
> eof
>

The trick is to try to follow exactly the table at the top of p. 89 of the
Amber Users' Manual (version 9; the equivalent info is pretty well hidden in
version 8). According to that, here is what should work:

  title goes here <-- "title"
 &cntrl <-- cntrl namelist
    nmropt=1,
    imin=0,
    irest=0,

    ....

    ntr=1,
 /
 &wt type='END', / <-- varying conditions
LISTOUT=POUT <-- file redirection
DISANG=../RST.dist
                                             <-- end of file redirection cards
 keep main chain atoms frozen <-- group information
 500.0 <-- see note below
FIND
* * M *
SEARCH
RES 20 145
END
END

I ran this on a test case, and it seemed to work fine.

[A note: 500 is a very large force constant for the restraints. A value
10-50 times smaller will serve to effectively keep the backbone fixed (say to
within 0.1 Ang.) while giving much less opportunity for dynamics problems to
arise because of the strong constraints.]

Please let me know if you still have problems!

...regards....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu