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
