AMBER Archive (2008)

Subject: Re: AMBER: problem with group input

From: anna.schrey_at_gmx.de
Date: Mon Jan 21 2008 - 08:22:48 CST

hi Ed,

when I see it right you did not set ntr=1. This flag has to be set for harmonic constraints.

about pmemd: I donīt know if this bug has already been fixed, but in AMBER9 it was not possible to run pmemd with harmonic and nmropt restraints at one time.

regards,

Anna
-------- Original-Nachricht --------
> Datum: Sun, 20 Jan 2008 22:53:28 -0800 (PST)
> Von: Ed Pate <pate_at_math.wsu.edu>
> An: amber_at_scripps.edu
> Betreff: AMBER: problem with group input

> Dear Amber community:
>
> I am trying to do a simulation of a protein-ligand complex in an explicit
> box of waters using sander and Amber8. I want to restrain most of the
> protein and to have NMR distance restraints on the ligand. My input
> parameter file follows:
>
> &cntrl
> imin=0,
> irest=0,
> ntx=1,
> ntt=1,
> temp0=300.0,
> tautp=1.0,
> ntp=1,
> taup=1.0,
> ntf=2,
> ntc=2,
> ntb=2,
> dt=0.002,
> nstlim=1000,
> ntwe=0,
> ntpr=10,
> nmropt=1,
> lastist=30000000,
> lastrst=30000000,
> &end
> &ewald
> &end
> &wt
> type='END',
> &end
> LISTOUT=/home/pate/sl2_myosin.d/POUT
> DISANG=/home/pate/sl2_myosin.d/RST
> restrain the following
> 1.0
> RES 1 58
> RES 137 207
> RES 215 617
> RES 636 715
> END
>
>
> The test simulation runs to completion. Checking the md.out file, the
> simulation invoked the NMR restraints. However, it did not appear to take
> the group input (no statement in the output file about the group residues
> and harmonic restraints.)
>
> I would greatly appreciate it if someone could point me in the right
> direction for the correct input file.
>
> One other question: It would probably be better to do this simulation
> using pmemd (one problem at a time). Would the input file be the same?
>
> Thanks for the help.
>
> Ed Pate
>
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-- 
Dr. Anna Katharina Schrey
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