AMBER Archive (2009)

Subject: Re: [AMBER] Restraint Mask length restriction !!

From: Sampath Koppole (sampathkoppole_at_yahoo.com)
Date: Mon Mar 09 2009 - 09:06:23 CDT

Dear Dr. Case,
Thank you very much for your prompt reply.
I am trying to put constraints such that restraints are put such that symmetrical groups are free rotate but the main group cannot move away from its position.
My restrained mask in my minimization script reads as follows :

Initial Structural Minimization with explicit water
 &cntrl
  imin=1, maxcyc=5000, ncyc=500, ntmin=1,
  ntb=1, cut=15, ntpr=10, ntr=1,
  RESTRAINT_WT=1.0,
  RESTRAINTMASK="(:2-150) & ! (:PHE_at_CE=,CD= | :TYR_at_CD=,CE= | :ASP_at_OD= | :GLU_at_OE= | :ARG_at_NH= | :ASN_at_ND2,OD1 :GLN_at_NE2,OE1 | :HIE_at_ND1,CD2,CE1,NE2 | :HID_at_ND1,CD2,CE1,NE2 | :HIP_at_ND1,CD2,CE1,NE2 | @H= | :150_at_O)",
/

In my mini.out file, the restrained mask (in bold) I see that is being processed is only the first 80 characters or so :
          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------
| Run on 03/09/2009 at 14:52:07
  [-O]verwriting output

File Assignments:
| MDIN: mini.in
| MDOUT: output/mini.out
|INPCRD: bak.inpcrd
| PARM: bak.prmtop
|RESTRT: output/mini.rst
| REFC: bak.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: output/mini.mdcrd
|MDINFO: output/mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

|INPTRA: inptraj
|
 
 Here is the input file:
 
Initial Structural Minimization with explicit water
 &cntrl
  imin=1, maxcyc=5000, ncyc=500, ntmin=1,
  ntb=1, cut=15, ntpr=10, ntr=1,
  RESTRAINT_WT=1.0,
  RESTRAINTMASK="(:2-23,33-150) & ! (:PHE_at_CE=,CD= | :TYR_at_CD=,CE= | :ASP_at_OD= | :
/

As you see, I am using the Sander module available in Amber 9.

Thanks once again,
Cheers,
Sampath.

----- Original Message ----
> From: David A. Case <case_at_biomaps.rutgers.edu>
> To: AMBER Mailing List <amber_at_ambermd.org>
> Sent: Monday, March 9, 2009 2:43:34 PM
> Subject: Re: [AMBER] Restraint Mask length restriction !!
>
> On Mon, Mar 09, 2009, Sampath Koppole wrote:
> >
> > Is there a way to work around the "restraint mask length being limited
> > to 80 characters" limitation ? I have a complex a complex restrained
> > mask which is longer than 80 characters (~120 characters !!).
>
> The restraintmask limit is currently 256 characters in the code. But
> there might be a namelist limitation(?). Can you give details (exact
> input you are using, which program and which version of Amber)?
>
> ...thx...dac
>
>
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