AMBER Archive (2009)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Mar 09 2009 - 09:30:16 CDT

On Mon, Mar 09, 2009, Sampath Koppole wrote:

>
> In my mini.out file, the restrained mask (in bold) I see that is being processed is only the first 80 characters or so :

> 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= | :
> /

This doesn't mean anything. The code snippet that copies the input file
to the output only prints the first 80 characters (we should change
this.) But the full line should still be available to the program. Do
you have other evidence that your mask is not be processed correctly?

...dac

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