HI
What version of amber are you using, and if 16, does it have all patches
applied ? The nfe syntax has changed recently
Thanks
On 2/15/17 2:29 PM, Osman, Roman wrote:
> Hello,
>
> Perhaps someone can help in constructing the input for doing simulations in amber using a radius of gyration constraint.
>
> I have a peptide embedded in a micelle of about 100 DPC that was constructed in PACKMOL and then the entire system was placed in a periodic box with waters and ions. I would like to minimize and equilibrate the micelle so all the polar groups are on the outside layer of the micelle facing the water. It seemed to me that applying a radius of gyration constraint on the N atoms of the DPC would be the correct way.
>
> The manual is not clear of how to prepare the input. One version of it is:
> Minimization input file in explicit solvent
> &cntrl
> ! Minimization options
> imin=1, ! Turn on minimization
> maxcyc=5000, ! Maximum number of minimization cycles
> ncyc=2500, ! 100 steepest-descent steps, better for strained systems
> .
> .
> .
> owtnm='OH2', ! Water oxygens are named OH2
> /
> Protein posres
> 10.0
> RES 1 62
> END
> END
>
> variable
> type = R_OF_GYRATION
> i = (973:7377)
> r = (21.5)
> end variable
>
> But the last part is apparently not read. Moving it to the &cntrl section produces a read error.
>
> I found an update (from 2012?) that suggest a different form:
> http://ambermd.org/doc12/nfe.pdf
>
> which I added to the input but placing it inside the &cntrl section does not work and outside it seems not to be read.
> Here is the form:
>
> &colvar
> cv_type = R_OF_GYRATION
> cv_ni = 6405, cv_nr = 1
> cv_i = (973:7377)
> cv_r = (21.5)
> /
>
> I saw the short discussion on this topic in the archive but there was no resolution of how to do it.
>
> Of course if anybody has an idea how to optimize the micelle without the RofG constraint that would also be appreciated.
> Thanks for your help,
>
> Roman Osman
> Department of Structural and Chemical Biology
> Mount Sinai School of Medicine
> New York, NY 10029
> Tel: 212-659-8627
> Fax: 212-849-2456
> e-mail: roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
>
>
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Feb 15 2017 - 12:00:02 PST
