Hello Thomas,
Actually yes I forgot to set up the trp to 1, and there were no errors !
btw what's about the force of the restraints? I've just noticed that
even with the restraint_wt=5.0 applied on the backbone, the structure
does not move. What's the difference between 1 and 100 and when do I
need the strongest restraints ?
Enrico
Il giorno ven 21 lug 2023 alle ore 11:24 Steinbrecher, Thomas
<thomas.steinbrecher.roche.com> ha scritto:
>
> are you using ntr=1 ?
>
> though I'd be surprised if the program would not throw an error if ntr = 0 and restraint_wt or ...mask are being set.
>
> Kind Regards,
>
> Thomas
>
>
> On Fri, Jul 21, 2023 at 10:46 AM Enrico Martinez via AMBER <amber.ambermd.org> wrote:
>>
>> Dear Amber users !
>>
>> I am running molecular dynamics simulation with restrains selectively
>> applied on a N terminal alpha helix of the protein (residues from 171
>> to 195), adding to the input file :
>>
>> restraint_wt=5.0, restraintmask=':171-195'
>>
>> After a quick 10 ns MD I noticed that in spite of the restraints the
>> region still moves without any difference compared to unrestrained
>> MD. In the output log I see:
>>
>> RESTRAINT = 0.0000
>>
>> What should I change in the input file to activate the restraints ?
>>
>> Many thanks in advance
>>
>> Enrico
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> Dr. Thomas Steinbrecher
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 092/3.92
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
> mailto: thomas.steinbrecher.roche.com
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Received on Fri Jul 21 2023 - 03:00:02 PDT
