AMBER Archive (2008)

Subject: RE: AMBER: HOLD fixed vs restraint mask

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Oct 21 2008 - 13:33:32 CDT

Hi Taufik,

> Hold the DNA fixed
> 100.0
> RES 1 40
> Hold the protein fixed
> 100.0
> RES 41 154
> END
> END'
>
 
> rfree: Error decoding variable 2 2 from:
> Hold the

I believe that you need this all on 1 line so:

Hold the DNA fixed
100.0
RES 1 40 41 154
END
END

Although you might be better off using the restraint_mask syntax which would
be, I think, ':1-40,41-154' or you could just write this as ':1-154' I
assume...

Note 100.0 is probably too large a restraint for actual MD - you should
probably reduce this to 10.0 or less.

All the best
Ross

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|\oss Walker

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