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.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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Dec 09 2007 - 06:07:52 PST
