Error message from Verlet MD step

Rasmus Storjohann rstorjoh at sfu.ca
Fri Feb 6 19:51:32 EST 1998


I'm trying to modify the refine.inp script to include electrostatic 
interactions. I do it gradually like this:

      constraints interaction (all) (all) weights * 1. elec 0.0 end end
      constraints interaction   (ATTR ABS CHARge > $elec_cutoff) 
      				(ATTR ABS CHARge > $elec_cutoff) 
				WEIGhts ELEC 1.0 END END

lowering $elec_cutoff linearly from 0.8 to 0.0. Then I do this

      dynamics  verlet
         nstep=$nstep time=0.005 iasvel=current firstt=$bath 
         tcoup=true tbath=$bath nprint=$nstep iprfrq=0  
      end

It works fine for a while, I get a lot of this:

 NBONDS: found        0 intra-atom interactions
 NBONDS: found        0 intra-atom interactions
 NBONDS: found        0 intra-atom interactions

In the third iteration I get even more of that (i.e. in iteration #1 I 
get 168 lines of NBONDS...., iteration #2 150 lines, iteration #3 944 
lines), and shortly into the fourth iteration I get this:

 NBONDS: found       38 intra-atom interactions
 NBONDS: found       32 intra-atom interactions
 %ATMCHK-ERR: unknown coordinates for atom "    -70  -GLN -O   "
 %ATMCHK-ERR: Unknown coordinates
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 BOMLEV=    0 reached.  Program execution will be terminated.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 Subroutine DIE called . Terminating

Which atom I get the error on varies. Can somebody tell me what is going on?

Thanx (again)

Rasmus

 ____________________________________________________________________
        __		Rasmus Storjohann
       / /\		Institute of Molecular Biology
      / /  \		and Biochemistry
     / / /\ \		Simon Fraser University
    / / /\ \ \		Burnaby, British Columbia V5A 1S6
   / /_/__\ \ \		e-mail: rstorjoh at sfu.ca
  /________\ \ \	Phone: (604) 291-5657 / 415-0575
  \___________\/	FAX:   (604) 291-3765




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