AMBER Archive (2009)

Subject: [AMBER] Problem with GROUP input

From: Jordan, Brad (jbjordan_at_amgen.com)
Date: Wed Sep 09 2009 - 18:58:36 CDT

Hi all,

I'm trying to perform an annealing run with the ibelly option and am trying to fix everything but the sidechain atoms on residues 10 to 110 while allowing full motion of residue 126. I know there is a section in the manual on this, but it doesn't seem to work. Here is the text of my anneal.out file:

    LOADING THE BELLY ATOMS AS GROUPS

    ----- READING GROUP 1; TITLE:
 Group Input for Ligand
 GRP 1 RES 126 TO 126
      Number of atoms in this group = 52
    ----- READING GROUP 2; TITLE:
 Group Input for Protein Backbone:
      ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW

      GRAPH NAME = * SYMBOL = * TREE SYMBOL = S RESIDUE TYPE = *

      GRAPH NAME = * SYMBOL = * TREE SYMBOL = B RESIDUE TYPE = *

      GRAPH NAME = * SYMBOL = * TREE SYMBOL = 3 RESIDUE TYPE = *

      GRAPH NAME = * SYMBOL = * TREE SYMBOL = E RESIDUE TYPE = *

      ***PROBLEMS WITH GROUPRES ***** 0 0 0 0 0 0 0 0 0 0 0 0 0*******

      Number of atoms in this group = 0
    ----- END OF GROUP READ -----

And here is my anneal.in file:

&cntrl
  nstlim=15000, ntt=1,
  scee=1.2,
  ntpr=500, pencut=1.0,
  ipnlty=1, nmropt=1,
  vlimit=10, ibelly=1
  ntb=0,
  igb=0,
&end

#
#Simulated annealing protocol
# from steps 0 to 5000 : raise target temperature 10-400K
# from steps 5000 to 10000: leave at 400K
# from steps 10000 to 40000 : re-cool to low temperatures
#
&wt type='TEMP0', istep1=0,istep2=1000,value1=10.,value2=800., &end
&wt type='TEMP0', istep1=1001,istep2=3000,value1=800.,value2=800., &end
&wt type='TEMP0', istep1=3001,istep2=15000,value1=0.0,value2=0.0, &end

#
#Strength of temperature coupling
#
&wt type='TAUTP', istep1=0,istep2=3000,value1=0.2,value2=0.2, &end
&wt type='TAUTP', istep1=3001,istep2=11000,value1=4.0,value2=2.0, &end
&wt type='TAUTP', istep1=11001,istep2=13000,value1=1.0,value2=1.0, &end
&wt type='TAUTP', istep1=13001,istep2=15000,value1=0.05,value2=0.05, &end

#Restraint control - ramp up restraints over the first 3000 steps

&wt type='REST', istep1=0,istep2=3000,value1=0.1,value2=1.0, &end
&wt type='REST', istep1=3001,istep2=15000,value1=1.0,value2=1.0, &end

&wt type='END', &end
LISTOUT=POUT
DISANG=RST
Group Input for Ligand
 1.0
SEARCH
RES 126
END
Group Input for Protein Backbone:
 1.0
FIND
* * S *
* * B *
* * 3 *
* * E *
SEARCH
RES 10-110
END
END

I found an old post about patching the amber7/src/lib/rgroup.f file, but it still doesn't seem to work. Any ideas what is causing the error in the group selection? Any help would be greatly appreciated.

Thanks!

Brad

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber