Charles and Guillermo,
I'll try a slightly less banal question this time ...
I'm trying to generate an extended structure for a peptide with
aminoisobutyric acid (AIB) residues. Using the python interface I get a
result that looks very strange to my eye (visualized in pymol), whereas if
I use the "classic" xplor script I get a pdb file that looks like an
extended peptide. I should note that I neglected to patch the N-term with
an acetyl and amidate the C-term using the "classic" script, though I do
not believe this change explains the observation.
I'd prefer to use the python interface, so I am eager to determine what my
mistake is in the script. We would like to see reasonable extended
structures prior to feeding in NOE and dihedral restraints.
Thanks,
Justin
Scripts below
****
# this checks for typos on the command-line. User-customized arguments can
# also be specified.
#
xplor.parseArguments()
# Filename for output structures. This string must contain the STRUCTURE
# literal so that each calculated structure has a unique name. The SCRIPT
# literal is replaced by this filename (or stdin if redirected using <),
# but it is optional.
#
outFilename = "extended.pdb"
# The protocol module has many high-level helper functions.
import protocol
protocol.initRandomSeed(331) # set random seed
# Generate PSF from sequence (initialize the correct parameters as side
effect!)
seq = "ACE AIB AIB AIB AIB ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA"
import psfGen
psfGen.residueTypes['protein'].append("AIB")
import protocol
protocol.initTopology('protein')
protocol.initParams('protein')
xplor.command("""
topology
residue AIB
group
atom N type=NH1 charge=-0.36 end
atom HN type=H charge= 0.26 end
atom CA type=CT charge= 0.00 end
atom CB1 type=CT charge=-0.30 end
atom HB11 type=HA charge= 0.10 end
atom HB12 type=HA charge= 0.10 end
atom HB13 type=HA charge= 0.10 end
atom CB2 type=CT charge=-0.30 end
atom HB21 type=HA charge= 0.10 end
atom HB22 type=HA charge= 0.10 end
atom HB23 type=HA charge= 0.10 end
atom C type=C charge= 0.48 end
atom O type=O charge=-0.48 end
bond N HN
bond N CA
bond CA CB1 bond CB1 HB11 bond CB1 HB12 bond CB1 HB13
bond CA CB2 bond CB2 HB21 bond CB2 HB22 bond CB2 HB23
bond CA C
bond C O
improper HB11 HB12 CA HB13 !stereo CB1
improper HB21 HB22 CA HB23 !stereo CB2
end
end
""")
psfGen.seqToPSF(seq,amidate_cterm=True,startResid=0)
protocol.genExtendedStructure("extended_python.pdb")
****
topology
@TOPPAR:topallhdg.pro
residue AIB
group
atom N type=NH1 charge=-0.36 end
atom HN type=H charge= 0.26 end
atom CA type=CT charge= 0.00 end
atom CB1 type=CT charge=-0.30 end
atom HB11 type=HA charge= 0.10 end
atom HB12 type=HA charge= 0.10 end
atom HB13 type=HA charge= 0.10 end
atom CB2 type=CT charge=-0.30 end
atom HB21 type=HA charge= 0.10 end
atom HB22 type=HA charge= 0.10 end
atom HB23 type=HA charge= 0.10 end
atom C type=C charge= 0.48 end
atom O type=O charge=-0.48 end
bond N HN
bond N CA
bond CA CB1 bond CB1 HB11 bond CB1 HB12 bond CB1 HB13
bond CA CB2 bond CB2 HB21 bond CB2 HB22 bond CB2 HB23
bond CA C
bond C O
improper HB11 HB12 CA HB13 !stereo CB1
improper HB21 HB22 CA HB23 !stereo CB2
end
end
segment
name=" "
chain
@TOPPAR:toph19.pep
sequence AIB AIB AIB AIB ALA ALA ALA ALA ALA ALA ALA ALA
ALA ALA ALA ALA end
end
end
parameter
{====>}
@TOPPAR:parallhdg.pro {*Read
parameters.*}
end
{ Set force constants for S-S bond lengths and angles to zero }
parameter
bonds ( name SG ) ( name SG ) 0. 1.
angle ( name CB ) ( name SG ) ( name SG ) 0. 1
end
vector ident (x) ( all )
vector do (x=x/10.) ( all )
vector do (y=random(0.5) ) ( all )
vector do (z=random(0.5) ) ( all )
vector do (fbeta=50) (all) {*Friction coefficient, in
1/ps.*}
vector do (mass=100) (all) {*Heavy masses, in
amus.*}
parameter
nbonds
cutnb=5.5 rcon=20. nbxmod=-2 repel=0.9 wmin=0.1 tolerance=1.
rexp=2 irexp=2 inhibit=0.25
end
end
flags exclude * include bond angle vdw end
minimize powell nstep=50 nprint=10 end
flags include impr end
minimize powell nstep=50 nprint=10 end
dynamics verlet
nstep=50 timestep=0.001 iasvel=maxwell firsttemp= 300.
tcoupling = true tbath = 300. nprint=50 iprfrq=0
end
parameter
nbonds
rcon=2. nbxmod=-3 repel=0.75
end
end
minimize powell nstep=100 nprint=25 end
dynamics verlet
nstep=500 timestep=0.005 iasvel=maxwell firsttemp= 300.
tcoupling = true tbath = 300. nprint=100 iprfrq=0
end
flags exclude vdw elec end
vector do (mass=1.) ( name h* )
hbuild selection=( name h* ) phistep=360 end
flags include vdw elec end
minimize powell nstep=200 nprint=50 end
{*Write
coordinates.*}
write coordinates output=extended_classic.pdb end
***
_______________________________________________
Xplor-nih mailing list
[email protected]
https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
