AMBER Archive (2005)

Subject: Re: AMBER: Make Distance restraints for non-standard residues

From: David A. Case (case_at_scripps.edu)
Date: Fri Jun 10 2005 - 14:59:13 CDT

On Fri, Jun 10, 2005, gtg549i_at_mail.gatech.edu wrote:
>
> I try to use the "makeDIST_RST", but it give me the following info:
>
> > makeDIST_RST -upb 7col.dist -pdb compl_cP3.pdb -rst RST.dist
> # makeDIST_RST
> Currently configured for up to 5000 atoms
> Using MAP file /usr/local/amber8/dat/map.DG-AMBER
> ERROR no map function for H70 BE2 :data= 1 BE2 H70 2 MAA O6
> 3.0
>
> I guess this is because my residues are not standard residues (BE2 and MAA are
> two organic molecules).

If you have non-standard residues, you will need to input the restraints using
the "raw" restraint format described in the sander section in the manual,
rather than by using the makeDIST_RST program. The latter program is not
really designed for non-standard residues.

...dac
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