Re: [AMBER] Error of restraint of atom using "pmemd" program in Amber 11

From: dbaogen <dbaogen.gmail.com>
Date: Sat, 8 Dec 2012 09:53:03 +0800

Dear Jason,

        Thanks for your help. I used the input file you provided this time. The error message from output file using pmemd program is as following:

      
  ----- READING GROUP 1; TITLE:
   Restrain residue 918

     GROUP 1 HAS HARMONIC CONSTRAINTS 2.00000
 GRP 1 RES 918 TO 918
      Number of atoms in this group = 1
    ----- READING GROUP 2; TITLE:
   END

     GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000

     rfree: End of file on unit 5

Best wishes

Duan Baogen


From: Jason Swails
Date: 2012-12-07 20:30
To: dbaogen; AMBER Mailing List
Subject: Re: [AMBER] Error of restraint of atom using "pmemd" program in Amber 11



On Fri, Dec 7, 2012 at 5:42 AM, dbaogen <dbaogen.gmail.com> wrote:

Dear all,

           Due to the computational speed difference, I would like to use pmemd.MPI program rather than snader.MPI to carry out atom position restraint MD simulation. Using sander program, the input parameters for restraint are set like "ntr=1,restraintmask=':918',restraint_wt=2.0 " . Searching the archive in the website, the input parameters for pmemd calculation are set like this:



If you update to Amber 12, pmemd in that version has the ntr, restraintmask, and restraint_wt variables available just like sander.


&cntrl
  imin=0,irest=1,ntx=5,
  nstlim=500000,dt=0.001,
  ntc=2,ntf=2,
  cut=12.0, ntb=2, ntp=1, taup=2.0,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,
  ntr=1,
  temp0=310.0,
  /
  2.0
  RES 918
  END
  END



You are missing a title to this group card, and the second atom number in the RES range (it is _always_ a range). Try the following instead:


&cntrl
  imin=0,irest=1,ntx=5,
  nstlim=500000,dt=0.001,
  ntc=2,ntf=2,
  cut=12.0, ntb=2, ntp=1, taup=2.0,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,
  ntr=1,
  temp0=310.0,
  /
  Restrain residue 918
  2.0
  RES 918 918
  END

  END

HTH,
Jason


-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Dec 07 2012 - 18:00:01 PST
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