AMBER Archive (2005)

Subject: Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values?

From: Petr Kulhanek (kulhanek_at_chemi.muni.cz)
Date: Wed May 25 2005 - 06:56:34 CDT

Hello,

> Sorry to bother. I didn't express clearly previously. I wonder if
> Amber8 is able to constrain (not restrain) certain bond angles at some
> fixed values? Thanks a lot.

Sander and pmemd have capability to constrain only bonds (with ntc >
1). So, if you want to constrain something else in sander (e.g. angles)
you are out of luck. There are two possibilities how to solve your problem.

Firstly, you can use gibss from AMBER 6 distribution. If I am not wrong
this program is able to constrain angles.

The second solution could be based on our implementation of methods for
potential of mean force calculations into sander and pmemd. These
methods are based on constrained dynamics. Supported constraints are as
follows: distance, angle, and dihedral angle. In general, any number of
constraints can be used, however the code is not optimized for great
number of constraints. Currently, the implementation is in beta testing
and there is no written documentation for it. If you are still
interested to use this second approach please let me know.

Petr

>
>
> Best Regards,
> Li
>
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