AMBER Archive (2007)

Subject: Re: AMBER: problem with distance restraints

From: Ed Pate (pate_at_math.wsu.edu)
Date: Mon Jan 22 2007 - 16:29:15 CST

David:

Thanks for taking a look at my problem. I appreciate the help.

I apologize for being so dense on this one, but I still can.t get it to
work.

My input file for the DISANG assignment is now named RST to conform better
to the tutorials. I have also added a more complete pointer to RST to be
sure I am trying to read the right file. The assignment statement is
"DISANG=RST" in md.in.

I now to get the error message:

  PGFIO-F-239/namelist read/unit=33/entity name is not member of group.
  File name = /home/pate/sl2_myosin.d/RST formatted, sequential access
record = 3
  In source file _restal.f, at line number 302
done

Thanks again for the help.

Ed

The file named RST for the statement "DISANG=RST" follows:
&rst
   ixpk=0, nxpk =0, iat=11899, 1825, r1= 6.6,r2=7.6,r3=8.3,r4=8.8,
      rk2=0., rk3=32.,irg6=1, ialtd=0,
  &end
  &rst
   ixpk=0, nxpk=0, iat=11926, 2911, r1=3.76 , r2=4.76, r3=5.46, r4=5.96,
      rk2=0., rk3=32., irg6=1, ialtd=0,
  &end

My md.in file follows:
&cntrl
   ntc=2,
   ntf=2,
   cut=20.0,
   igb=2,
   saltcon=0.2,
   gbsa=1,
   ntpr=5,
   nstlim=100,
   dt=0.002,
   ntt=1,
   tempi=300.0,
   temp0=300.,
   tautp=2.0,
   ntx=1,
   irest=0,
   ntb=0,
   ntwx=2500,
   ntwr=1000
   nscm=1000,
   nrespa=2,
   ntr=1,
   nmropt=1,
   lastist=30000000,
   lastrst=30000000,
  &end
  &wt
   type='END',
  &end
LISTOUT=/home/pate/sl2_myosin.d/POUT
DISANG=/home/pate/sl2_myosin.d/RST
   restrain the following
   1.0
RES 1 1
RES 3 7
RES 18 43
RES 45 85
RES 91 100
END
END

Note: one of the responses on the web page indicates that the following
might be needed to terminate the &wt statement

&rst iat=0, &end

I added this to RST. The program now runs, but the md.out and POUT files
indicate no constraints were set.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu