AMBER Archive (2008)

Subject: AMBER: Restraining with PMEMD 10

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Oct 25 2008 - 04:32:39 CDT

Hope not to be posting what has already been clarified.

min1.out:

   Amber 10 SANDER 2008
          -------------------------------------------------------

| PMEMD implementation of SANDER, Release 10

| Run on 10/25/2008 at 10:58:05

  [-O]verwriting output

File Assignments:
| MDIN: min1.in
| MDOUT: min1.out
| INPCRD: complex_AA1_POP_BOX.inpcrd
| PARM: complex_AA1_POP_BOX.prmtop
| RESTRT: min1.rst
| REFC: complex_AA1_POP_BOX.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile

 Here is the input file:

Steepest-descent min to eliminate clashes
&cntrl
  imin=1, maxcyc=3000, ntmin=2,
  cut=10, ntb=1, ntpr=50,
  ntr=1, restraintmask=":79-340, 341"
  restraint_wt=32,
/

| ERROR: PMEMD 10 does not support restraint_wt option!
| Please use Amber 6/7 GROUP format instead.
| ERROR: PMEMD 10 does not support restraintmask option!
| Please use Amber 6/7 GROUP format instead.

 Input errors occurred. Terminating execution.

=============
I was (badly) unable to find a description of "Amber 6/7 GROUP
format". I found a thread alluding to possible bad compilation of
pmemd. The one I used (intel ifort, mkl) was suggested by Ross Walker

archive:
From: Francesco Pietra <chiendarret.yahoo.com>
Date: Sun Jun 01 2008 - 00:12:12 PDT

I used it some time ago quite successfully for production MD on a
parallel NUMA-type machine with dual-opteron 875.. This is the first
time I try with restraints on the same machine and compilation.

Thanks for indicating where the format of restraining should be, or
what else. As the procedure of restraining with this large system in a
lipidic membrane is quite long, I would like to carry it with pmemd.

francesco pietra
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