[xplor-NIH] building sidechains onto known backbone coordinates
Charles at Schwieters.org
Charles at Schwieters.org
Mon Jul 8 15:26:35 EDT 2002
------- Start of forwarded message -------
Envelope-to: Charles at Schwieters.org
Delivery-date: Mon, 08 Jul 2002 08:21:39 -0600
Date: Mon, 8 Jul 2002 14:22:29 GMT
From: <Charles at Schwieters.org>
To: shrivasi at helix.nih.gov
In-reply-to: <Pine.SGI.4.44.0207051537460.15251-100000 at helix.nih.gov> (message
from Indira Shrivastava on Fri, 5 Jul 2002 15:43:00 -0400)
Subject: Re: Xplor
CC: Charles at Schwieters.org
Content-Type: multipart/mixed;
boundary="++----------20020708102227-068566595----------++"
Hi Indira--
Here's a script which adds unknown atoms given some known positions.
I'l send the resulting pdb file separately.
Charles
- --
Charles Schwieters email: Charles.Schwieters at nih.gov
www: http://schwieters.org/cds
phone: (301) 402-4914 FAX: (301) 402-2867
rtf @TOPPAR:topallhdg_new.pro end
evaluate ($kbbang = 500.0)
evaluate ($kbbimp = 500.0)
!
! building-on sidechains, given known bb atoms (from pdb file only).
!
! to use: change the line with input.pdb appropriately.
! Output will be in out.pdb
!
! set constraints to only calculate necessary interactions
! (don't calc bb-bb interactions)
! don't make the improper interactions too strong: will torque bonds, angles
!
! to try: turn off vwd entirely in stage1!
!
! script based on Nilges et.al. script for random starting coords
!
! CDS 7/8/02
!
param @TOPPAR:parallhdg_new.pro end
segment
name=" "
SETUP=TRUE
chain
LINK PEPP HEAD - * TAIL + PRO END { LINK to PRO }
LINK PEPT HEAD - * TAIL + * END
FIRSt PROP TAIL + PRO END { nter for PRO }
FIRSt NTER TAIL + * END
LAST CTER HEAD - * END
SET ECHO=TRUE END
coor @input.pdb
end
end
delete select (name hd1 and resname his) end
!remove all hydrogens!
delete select (hydro) end
write psf output=l.psf end
param
! @TOPPAR:parallhdg_new.pro
bond CP NH3 $kbon 1.473 ! CP - proline at N terminus
angle CP CP NH3 $kang 103.2 ! CP - proline at N terminus
angle HA CP NH3 $kang 109.5 ! CP - proline at N terminus
angle CT NH3 CP $kang 112.0 ! CP - proline at N terminus
improper HC HC CT CP 50.0 0 -70.0 ! N-term Pro
improper HA HA CP NH3 $kchi 0 -70.874 ! CP methylene
end
coor @indira.pdb
vector do (fbeta=10) (not known) {*Friction coefficient for MD heatbath.*}
vector do (mass=100) (not known) {*Uniform heavy masses to speed*}
vector do (fbeta=0) (known) {*Friction coefficient for MD heatbath.*}
vector do (mass=0) (known) {*Uniform heavy masses to speed*}
{*molecular dynamics. *}
constraints fix (known) end
vector do (vx = 0) (known)
vector do (vy = 0) (known)
vector do (vz = 0) (known)
evaluate ($init_t = 1000 ) {* Initial simulated annealing temperature.*}
vector do (vx = maxwell($init_t)) (attr mass>0)
vector do (vy = maxwell($init_t)) (attr mass>0)
vector do (vz = maxwell($init_t)) (attr mass>0)
vector do (x=(random()-0.5)*20) (attr mass>0)
vector do (y=(random()-0.5)*20) (attr mass>0)
vector do (z=(random()-0.5)*20) (attr mass>0)
!try bonds first
flags exclude * include bond end
constraints
interaction (attr mass>0) (attr mass=0)
interaction (attr mass>0) (attr mass>0)
end
!mini powell
! drop=1e5
! nprint=1
! tolg=1e-5
! nstep=1000
!end
flags exclude * include bond angle dihe cdihe impr vdw end
!energy end
!mini powell
! drop=1e5
! nprint=1
! tolg=1e-5
! nstep=1000
!end
evaluate ($kbon = 0.00005 ) {* Bonds. *}
evaluate ($kang = 0.00005 ) {* Angles. *}
evaluate ($timestep = 0.04)
evaluate ($nstep = 100)
!constraints
! interaction (all) (all)
! weights bond $kbon angl $kang impr $kimp vdw 0 elec 0 end
!end
!dynamics verlet
! nstep=5000 timestep=$timestep iasvel=current
! tcoupling=true tbath=$init_t nprint=50 iprfrq=0
!end
while ($kbon < 0.01) loop stage1
evaluate ($kbon = min(0.25, $kbon * 1.25))
evaluate ($kang = $kbon)
evaluate ($kimp = $kbon/10)
noe scale * $knoe end
!restraints dihed scale 0. end
constraints
interaction (attr mass>0) (attr mass=0)
weights bond $kbon angl $kang impr $kimp vdw 5e-4 elec 0 end
interaction (attr mass>0) (attr mass>0)
weights bond $kbon angl $kang impr $kimp vdw 5e-4 elec 0 end
end
dynamics verlet
nstep=$nstep timestep=$timestep iasvel=current
tcoupling=true tbath=$init_t nprint=50 iprfrq=0
end
end loop stage1
parameter {* Parameters for the repulsive energy term. *}
nbonds
repel=0.9 {* Initial value for repel - modified later. *}
nbxmod=-3 {* Initial value for nbxmod - modified later. *}
wmin=0.01
cutnb=4.5 ctonnb=2.99 ctofnb=3.
tolerance=0.5
end
end
! add vdw and slowly increase its weight
parameter nbonds
atom cutnb 100 tolerance 45 repel=1.2
rexp=2 irexp=2 rcon=1.0 nbxmod 4
end end
flags exclude * include bond angle impr dihe cdihe vdw end
constraints
interaction (attr mass>0) (attr mass=0)
weights bond $kbon angl $kang impr $kimp vdw 0.002 elec 0 end
interaction (attr mass>0) (attr mass>0)
weights bond $kbon angl $kang impr $kimp vdw 0.002 elec 0 end
end
dynamics verlet
nstep=500 timestep=$timestep iasvel=current
tcoupling=true tbath=$init_t nprint=50 iprfrq=0
end
constraints
interaction (attr mass>0) (attr mass=0)
weights bond $kbon angl $kang impr $kimp vdw 0.005 elec 0 end
interaction (attr mass>0) (attr mass>0)
weights bond $kbon angl $kang impr $kimp vdw 0.005 elec 0 end
end
dynamics verlet
nstep=500 timestep=$timestep iasvel=current
tcoupling=true tbath=$init_t nprint=50 iprfrq=0
end
constraints
interaction (attr mass>0) (attr mass=0)
weights bond $kbon angl $kang impr $kimp vdw 0.01 elec 0 end
interaction (attr mass>0) (attr mass>0)
weights bond $kbon angl $kang impr $kimp vdw 0.01 elec 0 end
end
dynamics verlet
nstep=500 timestep=$timestep iasvel=current
tcoupling=true tbath=$init_t nprint=50 iprfrq=0
end
constraints
interaction (attr mass>0) (attr mass=0)
weights bond $kbon angl $kang impr $kimp vdw 0.5 elec 0 end
interaction (attr mass>0) (attr mass>0)
weights bond $kbon angl $kang impr $kimp vdw 0.5 elec 0 end
end
dynamics verlet
nstep=500 timestep=$timestep iasvel=current
tcoupling=true tbath=$init_t nprint=50 iprfrq=0
end
!flags exclude * include bond angle end
energy end
mini powell
drop=100
nprint=1
tolg=1e-5
nstep=10000
end
constraints
interaction (attr mass>0) (attr mass=0)
weights bond $kbon angl $kang impr $kimp vdw 0.1 elec 0 end
interaction (attr mass>0) (attr mass>0)
weights bond $kbon angl $kang impr $kimp vdw 0.1 elec 0 end
end
mini powell
drop=100
nprint=1
tolg=1e-5
nstep=10000
end
write coord output=out.pdb end
stop
-=- MIME -=-
This is a multi-part message in MIME format.
--++----------20020708102227-068566595----------++
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Hi Indira--
Here's a script which adds unknown atoms given some known positions.
I'l send the resulting pdb file separately.
Charles
--
Charles Schwieters email: Charles.Schwieters at nih.gov
www: http://schwieters.org/cds
phone: (301) 402-4914 FAX: (301) 402-2867
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--++----------20020708102227-068566595----------++--
------- End of forwarded message -------
--
Charles Schwieters email: Charles.Schwieters at nih.gov
www: http://schwieters.org/cds
phone: (301) 402-4914 FAX: (301) 402-2867
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