AMBER Archive (2008)

Subject: Re: AMBER: Constrained group

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Jun 30 2008 - 11:03:15 CDT

Hi Fatima -
Just back from short vacation and saw you were having trouble with this. In
example code of this sort that I have, the "END" keyword starts in column 1.
I would try that first; I am inferring that you are starting in column 2
here since it looks like you line up with the & in the namelists, which
should start in column 2. The doc for group namelists is not crystal clear
on this, but I basically use the same code as sander (or at least did in the
timeframe of amber 7), so I should be "in spec" on parsing the cards. Let
me know if that does not work.
Regards - Bob Duke

----- Original Message -----
From: <fatima.chami_at_durham.ac.uk>
To: <amber_at_scripps.edu>
Sent: Monday, June 30, 2008 5:54 AM
Subject: AMBER: Constrained group

>
>
> Dear Amber's users
>
> I am using the PMEMD to run a system with some residues hold fixed. The
> program
> read correctly the group of residues I specified in the input file but did
> not
> stop there...it continued to read the second group for some reasons
> despite the
> 'END' card.
> I copied the input file here:
> &cntrl
> imin = 0, ntb = 1,
> igb = 0, ntpr = 1000, ntwx = 4000,
> ntt = 3, gamma_ln = 1.0,
> tempi = 0.0, temp0 = 300.0
> nstlim = 1000000, dt = 0.001,
> cut = 12, iwrap = 0, ntr = 1
> /
> Hold the Edicols
> 500.0
> RES 1 144
> END
> END
> --------------------------------------------------
> I copied the last line of the output file:
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> Hold the Edicols
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
> GRP 1 RES 1 TO 144
> Number of atoms in this group = 5328
> ----- READING GROUP 2; TITLE:
> END
>
> rfree: End of file on unit 5
>
>
> ----------------------------------------------
> any ideas on what went wrong here ..please
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu