AMBER Archive (2008)

Subject: Re: AMBER: Restraining with PMEMD 10

From: Robert Duke (rduke_at_email.unc.edu)
Date: Sat Oct 25 2008 - 07:57:03 CDT

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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