Re: [AMBER] Center of mass restraints with pmemd.cuda

From: Kevin Hauser <84hauser.gmail.com>
Date: Wed, 4 Nov 2015 10:00:24 -0500

Hi,

The latest version of Amber does support the function you want. Is there
the letter "O" in your r2?

HTH,
Kevin

On Wed, Nov 4, 2015 at 9:57 AM, abdennour braka <
abdennour.braka.univ-orleans.fr> wrote:

> Dear Amber users,
> I tried to run a SMD using pmemd.cuda with the following restraint file:
>
> &rst iat=-1,-1, r2=5.O, rk2=7.2, r2a=0.5 ,igr1=5608,5609,5610,
> igr2=2387,2411,2762,2786,3024,3087,3106,3214, /
>
> I noticed that iat < 0 is not supported with pmemd.cuda.
> Is there another way to add Center of mass restraints that can work with
> pmemd.cuda?!!
>
> Thank you for any replies.
>
> A.BRAKA
>
> --
> Abdennour BRAKA
> /PhD Student/
> /Structural Bioinformatics & Chemoinformatics/
> /Institut de Chimie Organique et Analytique (ICOA)/
> /UMR CNRS-Université d'Orléans 7311/
> /Université d'Orléans/
> /Rue de Chartres/
> /F-45067 Orléans/
> /phone: +33 238 494 577/
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 



-- 
-- - -
HK
════════════════════════════════════════════
Kevin E. Hauser, Ph.D. Candidate
NRSA Fellow, National Institutes of Health
Carlos Simmerling Laboratory
Miguel Garcia-Diaz Laboratory
100 Laufer Center for Physical and Quantitative Biology
Stony Brook, New York 11794-5252
Phone: (631) 632.5394  Email:  84hauser.gmail.com
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Received on Wed Nov 04 2015 - 07:30:04 PST
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