Re: AMBER: Offending restraints????

From: <saccenti.cerm.unifi.it>
Date: Wed, 27 Jun 2007 11:33:16 +0200 (CEST)

Yes I know that this doesnt make sense but I'm mimicking a very bad
protein assignement..

anyway I tried to use the -ual option but I get the error:

# makeDIST_RST
Currently configured for up to 5000 atoms
Using MAP file ./map.DG-AMBER
parse_ual: ERROR UAL data not in 8(7) column format: ( 33 MET HN 33
MET QG 2.27
) ()

my input file is in the format

 33 MET HN 33 MET QG 2.27
 12 ARG HN 12 ARG QD 2.21
 56 SER HA 57 VAL QG2 2.19
 39 GLU QG 40 ARG HN 6.99

and it works when using the -pdb option

I checked in the archive and found an example and I see that I miss the
8th coloumn but I do no know to what the last coloumn must refer.

Many thanks
for the help

Edo



> On Tue, Jun 26, 2007, saccenti.cerm.unifi.it wrote:
>>
>> These values come for experimental NMR restrains that have been randomly
>> perturbed.
>
> Does it really make sense to have perturbations that then give upper
> bounds
> between non-bonded atoms of 1.2 Ang? I think you will just get horrible
> energies and very unstable simulations.
>
> You might try using the -ual option to makeDIST_RST: that will use the
> lower
> bounds you provide, rather than assuming a default lower bound.
>
> ...dac
>
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-- 
Dr Edoardo Saccenti
CERM Magnetic Resonance Center
University of Florence
Fiorgen Foundation
Via Luigi Sacconi n 6
50019 Sesto Fiorentino
(FI) Italy
Tel: +39 055 4574281
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Received on Sun Jul 01 2007 - 06:07:05 PDT
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