jayant james wrote:
Hi!
I have two phosphorylated serines which form part of peptide that I want
to perform simulated annealing. But the catch is the SEP group is read
as a Non-Protein and so it is present in two T-coupling groups, the
Non-Potein and the protein group I want to heat. I need to remove this
group (SEP-phosphorylated serine) from the Non-Protein group. The
Non-Protein group contains about 20,000 atoms (water, counterions and
also the SEP group). So how can I remove this group from the Non-Protein
group?
Add it to aminoacids.dat, and increment the number at the top of the file.
-Justin
Welcoming your suggestions
Jayant James
On Sat, Mar 21, 2009 at 4:52 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
jayant james wrote:
Hi !
I am attempting to do a simulated annealing and running into
problem.
Let me give a introduction to my system. I have a segment of a
protein that was not crystallographyically resolved, but was
later resolved by NMR.
So I ligated the NMR structure to the crystal structure and in
an attempt to find the correct orientation of the NMR segment in
the crystal structure I planned to do a simulated annealing run
specifically to this ligated NMR segment. Having ligated this
NMR segment to the crystal structure I gave the pdb2gmx command,
then created a box, filled it with water and performed a
distance restrained energy minimization (wherein I input some
FRET distances as distance restraints). Its all fine till this
step. Now I create an index group that has the NMR group as the
third group in the temperature coupling, the other two are
Protein and Non-Protein. when I run the grompp to start a
simulated annealing run I get a message stating that the NMR
group's atoms are also found in the Protein group. Gromacs is
right in detecting this problem. As I cannot have the same amino
acids in 2 different groups which are coupled to two different
temperatures. So how am I to attempt this simulated annealing
because the program does not want to have the NMR group present
in the Protein group?
You will need to make special index groups, i.e.:
r 1-x (for the appended segment)
r x-y (the rest of the protein)
These groups can be used as your tc-grps.
-Justin
So say I delete the NMR segment that was appended to the crystal
structure how and which stage do I integrate the NMR group that
I wanted to perform the simulated annealing on, into the system?
Thanks
Jayant
*The pr.mdp file is as below*
; Berendsen temperature coupling is on in two groups
Tcoupl = Berendsen
tc-grps = Protein Non-Protein NMR-group
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Energy monitoring
energygrps = Protein Non-Protein NMR-group
; Pressure coupling is not on
Pcoupl = parrinello-rahman
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
;
;
;
;simulated annealing
;Type of annealing form each temperature group (no/single/periodic)
annealing = no no single
;
;Number of annealing points to use for specifying annealing in
each group
annealing_npoints 0 0 9
;
; List of times at the annealing points for each group
annealing_time = 0 25 50 75 100 125 150 175 200
; Temp.at each annealing point, for each group.
annealing_temp = 300 350 400 450 500 450 400 350 300
*The error messge is given below*
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_D 1
Excluding 2 bonded neighbours for SOL 72948
Excluding 1 bonded neighbours for NA+ 214
Excluding 1 bonded neighbours for CL- 207
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
# G96BONDS: 4588
# G96ANGLES: 6638
# PDIHS: 2521
# IDIHS: 2044
# LJ14: 7634
# DISRES: 22
# SETTLE: 72948
initialising group options...
processing index file...
WARNING 1 [file "new.top", line 28039]:
T-Coupling group Protein has fewer than 10% of the atoms (4550
out of
223817)
Maybe you want to try Protein and Non-Protein instead?
WARNING 2 [file "new.top", line 28039]:
T-Coupling group Non-Protein has fewer than 10% of the atoms (2
out of
223817)
Maybe you want to try Protein and Non-Protein instead?
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: readir.c, line: 843
Fatal error:
Atom 2589 in multiple T-Coupling groups (1 and 3)
-------------------------------------------------------
** ** *The commands that I use are given below*
** #pdb2gmx -f start.pdb -p new -o new -ignh -merge
#creating a box and addition of water molecules
#editconf -f new.gro -o out -c -princ -d 2.2
#genbox -cp out -cs -o check
#editconf -f check -o check.pdb
#rasmol check.pdb
#Energy minimization and addition of ions to neutralise the system
#grompp -f em.mdp -c check -p new.top -o em.tpr
#genion -s em.tpr -o next -p new -random -g -neutral -conc 0.15
#pname -Na -np 13
#editconf -f next.gro -o next.pdb
#rasmol next.pdb
#option 13 for SOL
#Running the EM. Here change the Na to NA+ in topology file and
I/P *.gro file.
#grompp -f em.mdp -c next.gro -p new.top -o em.tpr
#mdrun -v -s em -x em -o em -c em.gro &
#editconf -f em.gro -o em.pdb
#rasmol em.pdb
*This is where the problem begins*
#Running MD.
grompp -f pr.mdp -c em.gro -o pr.tpr -p new.top -n index
#mdrun -s pr -e pr -g md -o traj.trr -c pr.gro &
#extending
#tpbconv -s ../pr.tpr -f 300.xtc -e ../ener.edr -o 1ns.tpr
-until 1000
#mdrun -s 1ns.tpr -o 1ns.trr &
--
Jayasundar Jayant James
www.chick.com/reading/tracts/0096/0096_01.asp
<http://www.chick.com/reading/tracts/0096/0096_01.asp>
<http://www.chick.com/reading/tracts/0096/0096_01.asp>)
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Jayasundar Jayant James
www.chick.com/reading/tracts/0096/0096_01.asp
<http://www.chick.com/reading/tracts/0096/0096_01.asp>)
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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