AMBER Archive (2005)

Subject: Re: AMBER: FW:

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 19 2005 - 21:46:48 CDT

On Wed, Jul 20, 2005, Andrew Box wrote:
>
> I created a new map file by copying over the map data for the DNA
> base into a new file, then I typed in the data for my anti-cancer
> drug (included as attachments are the pdb file of the complex and,
> the 7 column restraint file and the map file).

You should make your drug look just like a "residue" in the map file. What
you had is this:

BEN HC = HC
BEN HN = HN
BEN H1 = H1
BEN H2 = H2
BEN H6 = H6
BEN H9 = H9
BEN Q10 = H101 H102
BEN M13 = H131 H132 H133
BEN H14 = H14
BEN H15 = H15
BEN Q16 = H161 H162
BEN H17 = H17
BEN M18 = H181 H182 H183
BEN H19 = H19
BEN M20 = H201 H202 H203
BEN Q21 = H211 H212
BEN H22 = H22
BEN Q28 = H281 H282
BEN M31 = H311 H312 H313
BEN H83 = H83
BEN H84 = H84

RESIDUE DA
MAPPING H8 = H8
MAPPING H2 = H2
MAPPING H1' = H1'
MAPPING H2' = H2'1
MAPPING H2'1 = H2'1
MAPPING H2'' = H2'2
MAPPING H2'2 = H2'2
MAPPING H3' = H3'
MAPPING H4' = H4'
MAPPING H5' = H5'1
MAPPING H5'1 = H5'1
MAPPING H5'' = H5'2
MAPPING H5'2 = H5'2
MAPPING Q2' = H2'1 H2'2
MAPPING Q5' = H5'1 H5'2
MAPPING P = P
MAPPING H61 = H61
MAPPING N1 = N1

....

but what you need is something like this at the top:

RESDIUE BEN
MAPPING HC = HC
MAPPING HN = HN

...etc.

That is, do the same thing for BEN that you see for DA. "MAPPING" is a
keyword that needs to be there in the input.

....dac

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