AMBER Archive (2007)

Subject: Re: AMBER: protein_model

From: steinbrt_at_scripps.edu
Date: Sat Dec 08 2007 - 12:51:35 CST

Dear Ursula,

take a look at the restraintmask and restraint_wt keywords in the
restraints section of the manual. You would specify the backbone atom with
a mask that looks like ':1-100_at_CA,C,N' for backbone atoms of residue 1 to
100. Please be aware that a force constant of 1000 kcal/molA**2 is
extremely strong and might even lead to simulation problems. Setting a
harmonic restraint of 10 kcal will already allow almost no movement of the
constrained atoms. If you want to keep atoms absolutely fixed, consider
using the ibelly command.

> I would like to constrained the backbone atoms with a force constant of
> 1000 so that only the
> side chains were able to move freely during the simulation. Can someone
> help me how could I
> define this part in my input file?
>
> thank you in advance for any help
>
>
> Best Regards,
> Urszula Uciechowska
>
> MSc.PhD Student
> Medicinal Chemistry Group
> University of Halle-Wittenberg
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