AMBER Archive (2005)

Subject: AMBER: Atoms restrain

From: Angelo Pugliese (angelo_at_holmes.cancres.nottingham.ac.uk)
Date: Mon Dec 19 2005 - 07:09:35 CST

Dear Amber Users,

Below there is the input file for a MD equilibration step in which I
want to restrain my 24 residues dsDNA with 5.0 kcal/mol weight and let
the water molecules and the counterions be free to move. Within the DNA
I want to restrain four C1' atoms with a different weight (10.0) in
order to keep the helix overtwisted as I set previously by nucgen.
I wonder if my input file is correct, i mean I am afraid that the
restrain on the whole DNA will overwrite the restrain on the single
atoms and therefore messing up everything.
Thank you for your precious suggestions.
This is the input:

MD on water and counterions
 &cntrl
    irest=1, ntx=7,
        ntf=2, ntb=2, scee=1.2, cut=9.0,
        ntr=1,
        nstlim=5000, dt=0.002,
        temp0=300.0, ntt=1,
        ntp=1,
        ntc=2,
 &end
Atoms that are going to be restrained in the MD simulation
5.0
RES 1 24
END
Restrain on the C1' atoms
10.0
ATOM 9 9 355 355 386 386 740 740
END
END

This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu