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