AMBER Archive (2002)

Subject: input format for gibbs restraints

From: Jose Ramon Blas (jramon_at_ub222059.pcb.ub.es)
Date: Wed Nov 13 2002 - 20:59:43 CST

Hi all,

In the manual:
----------------------------------------------------------------
Restraint/constraint definitions must be entered in the formatted
form shown below, not in a namelist.

Restraints/constraints are read in as pairs of lines:

    line A: IAT1,IAT2,IAT3,IAT4,IUMB,IZE,ITOR,RLMDA1,RLMDA
    FORMAT (7(I5,1X),2F10.5)
    line B: RKEQ1,REQ1,RKEQ2,REQ2,IPER,IPER2
    FORMAT (4F10.5,2I5)

As many restraints/constraints may be defined as are desired.
A blank record signals the end of the input. This data must be
entered in the formatted form shown.
It does not support a namelist convention.
----------------------------------------------------------------

My input:
----------------------------------------------------------------
# FEP del monomer amb q -1
 &cntrl
         timlim=999999., ibelly=0, iewald=0,
         ntx=7, ntxo=1,
         ntb=0, iftres=1,
         nrun=41, ntt=1, temp0=298.0,
         ntp=0, taup=0.4,
         nstlim=10000, init=4, dt=0.002,
         ntc=3, ncorc=1, itimth=1,
         ntf=3, idiel=1, idsx0=-1, ioleps=0, intprt=1,
         cut=1000, scnb=2.0, scee=1.2, dielc=1.0,
         ntpr=100, ntwx=10000, ntwv=-1, ntwe=10000, isande=1,
         ntr=1,
         almda=1.00, almdel=-0.025, isldyn=-3, idifrg=1, nstmeq=5000,
         nstmul=5000, idwide=1,
         nstpe=5000, nstpa=5000,
         iperat=1, iatcmp=1,
 &end
Restraints applied
   10 11 13 14 0 0 0 1.00000 0.00000
 100.00000 0.00000 100.00000 0.00000 0 0

------------------------------------------------------------------------

My error:
------------------------------------------------------------------------
   5. REFERENCE ATOM COORDINATES

  Restraints applied
     GROUP 1 has harmonic restraints 10.00000

     ERROR IN EXTRACTING THE VARIABLE NUMBER 2 FROM
      100.00000 0.00000 100.00000 0.00000 0 0
     IN SUBROUTINE RFREE *** CHECK INPUT
-------------------------------------------------------------------------

I have looked also at the misc.f program (line 290) where the message
comes from, but no idea on what is the reason for it?

Format is exactly as specified in the User's Manual.

Thanks a lot for any suggestions,

Jose Ramon

---------------------------------------------------------------------------
Jose R. Blas
Molecular Modelling & Bioinformatics e-mail: jramon_at_mmb.pcb.ub.es
IRBB, Parc Cientific de Barcelona phone: + 34 93 403 71 55
C/Josep Samitier 1-5,
08028 Barcelona