[AMBER] Simulations with R_OF_GYRATION

From: Osman, Roman <roman.osman.mssm.edu>
Date: Wed, 15 Feb 2017 19:29:30 +0000


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
    ! 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
RES 1 62

   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:

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:

   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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Received on Wed Feb 15 2017 - 11:30:03 PST
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