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Hello Yi--
> I am now modifying the script 'dock_tor_rigid.py' from eginput/
> dock_dipolar_chemshift. To perform minimization of the oligomer, I added
> lines as follows:
>
> command("""
> ncs restraints
> initialize
> group
> equi (segid A)
> equi (segid B)
> equi (segid C)
> equi (segid D)
> ...
> weight = $kncs
> end
> ?
> end""")
you should set weight = 1, and then manipulate the ncs term in the
Python interface:
ncs = XplorPot("NCS")
ncs.setScale(10)
potList.append( ncs )
> ...
> m.fix( select('resid 5:20') )
> groupList = m.groupList()
> groupList.append( select('resid 25:43') )
> groupList.append( select('resid 5:20'))
the last line is redundant. You want:
m.fix( 'resid 5:20' )
m.group( 'resid 25:43') )
protocol.cartesianTopology(m)
Then residues 5 to 20 won't move, 25 to 43 will move as a rigid body and
residues in between will move using all degrees of freedom (meaning that
you will need BOND, ANGL, and IMPR terms in addition to any other.
You usually want to make sure you don't have any of these messages:
> ...
> AT_Build::buildNode: cycle link found between atoms 11538 GLY 21 N and 11536
> PHE 20 C
> removing bond.
> Node info:
> node 0 0: -1 (base atom), 19 SER 5 N, 20 SER 5 HN, 21 SER 5 CA, 22 SER 5
> HA, 23 SER 5 CB, 24 SER 5
> node 1 0: 17 ILE 4 C, translate
> node 1 1: 301 GLY 21 N, translate
> ...
> node 26 16: 11539 GLY 21 HN, translate
>
> total number of degrees of freedom: 5784
> *-- POWELL ------ step= 0 --- stepsize! = & nbsp; 0.01000 --- energy
> evals= 2 -*
> | E(poten)=882181.6704152 grad= 98.1839386 VDW=
> 882181.6704152 |
> *------------------------------------------------------------------------------*
> ...
> --------------- cycle= 1
> --------------------------------------------------
> | Etotal =0.29E+10 grad(E)=79.202 E(VDW )=444532.967 E(NOE )=
> 0.000 |
> | E(RAMA)=0.000 E(COLL)=0.29E+10 E(SANI)=
> 0.000 |
>
> -------------------------------------------------------------------------------
> dock.py(399): rms_bonds = command("print thres=0.05 bonds","result")
> (atom-i |atom-j ) dist. equil. delta energy const.
>
> (A 4 C |A 5 N ) 371.521 1.329 370.192 ******** 1000.000
> (A 20 C |A 21 N ) 397.705 1.329 396.376 ******** 1000.000
> (A 24 C |A 25 N ) ******** 1.329 ******** ******** 1000.000
> (A 44 N |A 44 HN ) 75.604 0.980 74.624 ******** 1000.000
> (A 44 N&! nbsp;&nb sp; |A 44 CA ) 81.043 1.458 79.585
> ******** 1000.000
> ...
> I am not sure what's going on here, but apparently something has gone quite
> wrong. What have I missed?
you need to include the terms I listed above for, otherwise bad things
happen.
> It seems that I should add the posSymmPot, is there an example?
The NCS term is taking the place of that term here. What you probably do
want, though are symmetry distance restraints. For a symmetry dimer with
segids A and B, this can be
from distSymmTools import create_DistSymmPot, genDimerRestraints
dSymm = create_DistSymmPot('dSymm')
for r in genDimerRestraints(segids=['A','B'],
resids=range(10, # start residue number
380, # final residue number
10)):
dSymm.addRestraint(r)
pass
dSymm.setShowAllRestraints(True)
dSymm.setEnsembleAveType("average")
dSymm.setScale(100)
potList.append(dSymm)
You might add these pairwise to your four subunits:
A<->B, B<->C, C<->D, D<->A
> Why is the bond between resid 20 and 21 removed?
This is not a potential energy bond term, but rather a link in the
IVM. It should be removed using the IVM setup I listed above, so there
should be no message. The fact there's a message usually means
something's not quite consistent
> The degree of freedom is definitely wrong, did I did the NCS part wrong?
I can't comment on whether or not they're correct, but those degree of
freedom have nothing to do with the NCS setup: they are the IVM degrees
of freedom: three for each free atom, 6 for a rigid body with more than
3 atoms and 0 for the fixed region.
best regards--
Charles
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