AMBER Archive (2007)

Subject: Re: AMBER: Offending restraints????

From: saccenti_at_cerm.unifi.it
Date: Tue Jun 26 2007 - 10:36:44 CDT

I genetated them using the command:

/makeDIST_RST -upb modified.upl.shft -pdb ../PDB/PDB01/prm_1.pdb -map
./map.DG-AMBER -rst RST

thanks
edo

> you do indeed have multiple restraints with R3<R2. this won't work.
> I don't know how you generated them so cannot help but there is
> a problem with the DISANG data.
> example from your file:
> r1= 1.30, r2= 1.80, r3= 1.21, r4= 1.71,
>
> On 6/26/07, saccenti_at_cerm.unifi.it <saccenti_at_cerm.unifi.it> wrote:
>>
>> I'm a recent amber user, anyway I'm not declaring IFVARI
>> so I suppose it is assumed to be 0
>>
>> I attach my DISANG file
>>
>> Really many thanks
>> Edo
>>
>>
>>
>>
>> > can you show us the actual restraint input from the DISANG file?
>> > do you have ifvari = 0 or 1?
>> >
>> >
>> > On 6/26/07, saccenti_at_cerm.unifi.it <saccenti_at_cerm.unifi.it> wrote:
>> >>
>> >> Dear all,
>> >> I'm gettig this error when staring a minimization:
>> >>
>> >> What's wrong?
>> >>
>> >> Note that this upls have been "perturbed" so that
>> >> that the actual 33 MET HN 33 MET QG 2.27
>> >> was indeed 33 MET H 33 MET QG 4.54
>> >>
>> >> Maybe 2.27 is so tight that Amber refuses it?
>> >>
>> >> many many Thanks
>> >> Edo
>> >>
>> >> >>>
>> >> Here are comments from the DISANG input file:
>> >> #
>> >>
>> >> # 33 MET HN 33 MET QG 2.27
>> >>
>> >>
>> >> ERROR: r1 -> r4 (and r1a -> r4a) must be monotonically increasing;
>> >> Offending restraint:
>> >> ******
>> >> HB ( 812)-COM ( -1) NSTEP1= 0
>> NSTEP2=
>> >> 0
>> >> R1 = 1.300 R2 = 1.800 R3 = 1.610 R4 = 2.110 RK2 = 20.000 RK3
>> =
>> >> 20.000
>> >>
>> >>
>> >>
>> >> --
>> >> 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
>> >>
>> >> -----------------------------------------------------------------------
>> >> The AMBER Mail Reflector
>> >> To post, send mail to amber_at_scripps.edu
>> >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>> >>
>> >
>> >
> 

-- 
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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu