AMBER Archive (2008)

Subject: RE: AMBER: Restraining with PMEMD 10

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Oct 25 2008 - 12:25:08 CDT

Hi Francesco,

The group specs go after the / of the cntrl namelist. See tutorial B1 for an example:

http://ambermd.org/tutorials/basic/tutorial1/section5.htm

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Francesco Pietra
> Sent: Saturday, October 25, 2008 9:34 AM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Restraining with PMEMD 10
>
> Hi:
> Could you please check this (ban) min.in:
>
> Steepest-descent min to eliminate clashes
> &cntrl
> imin=1, maxcyc=3000, ntmin=2,
> cut=10, ntb=1, ntpr=50, ntr=1,
> Title one
> RES 79 100
> END
> Title two
> RES 100 200
> END
> Title three
> Res 200 300
> END
> Title four
> Res 300 340
> END
> Title five
> Res 341
> END
> Weight
> WT 32
> END
> END
> /
>
> ERROR: too many values for NAMELIST variable, unit 5, file
> .../min1.in, line 5, position8. Should it not be basically wrong
> (which I doubt), how many residues are allowed per "Title"?
>
> Thanks
> francesco
>
> On Sat, Oct 25, 2008 at 2:57 PM, Robert Duke <rduke_at_email.unc.edu> wrote:
> > I believe the relevant appendix was dropped to keep the manual under 50
> > pounds... Look at the amber website, ambermd.org. Then look under the
> > heading "The program package" and follow the link "Amber 8 Manual".
> Under
> > this select the amber 8 manual again, and open the appendices bookmark.
> Then
> > go to Appendix B: GROUP Specification.
> > Regards - Bob Duke
> > ----- Original Message ----- From: "Francesco Pietra"
> > <chiendarret_at_gmail.com>
> > To: "Amber" <amber_at_scripps.edu>
> > Sent: Saturday, October 25, 2008 5:32 AM
> > Subject: AMBER: Restraining with PMEMD 10
> >
> >
> >> 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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> >
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