<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear all, <br>
i
want to simulate a protein solvated in water. I have downloaded the
protein coordinate from RCSB protein data bank (ID 2KB7).
These has 20 merged coordinate & i have taken conformer #6. Then i
run pdb2gmx with ffG43a1 & solvate the protein with spc waters.
Next i energy minimize the system with emtol=150.<br>
--------------------------------------------------------------------------------------------------------------<br>
Polak-Ribiere Conjugate Gradients converged to Fmax < 150 in 59 steps<br>
Potential Energy = -4.1081506e+05<br>
Maximum force = 1.3278603e+02 on atom 213<br>
Norm of force = 1.1614658e+01<br>
<br>
Performed 72 energy evaluations in total.<br>
-------------------------------------------------------------------------------------------------------------<br>
With the energy minimized structure i then run position restraint
simulation, with fc=1000 peptide heavy atom. It gives lots of
LINCS WARNING, wich involvs mainly backbone C O N H atoms. Then i
have added hydrogen bond constraints & NOE distance restraints as
given in the protein data bank and also added phi psi dihedral
restraints. Even though i have got the LINCS WARNING involving backbone
C O N H.<br>
------------------my <span style="font-weight: bold;">pr.mdp</span>--------------<br>
title = sp position restraining<br>
cpp = /usr/bin/cpp<br>
define = -DPOSRES<br>
constraints = all-bonds<br>
constraint_algorithm= lincs<br>
lincs_order = 4<br>
lincs_iter = 1<br>
lincs_warnangle = 30<br>
integrator = md<br>
dt
= 0.002 ; ps !<br>
nsteps = 250000 ; total 1 ns<br>
nstcomm = 1<br>
nstxout = 1000<br>
nstvout = 1000<br>
nstfout = 0<br>
nstlog = 1000<br>
nstenergy = 1000<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 0.9<br>
rcoulomb = 0.9<br>
vdwtype = Cut-off<br>
rvdw = 1.2<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
coulombtype = PME<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
;distance restraints NMR refinement<br>
disre = simple<br>
disre_weighting = equal<br>
disre_fc = 1000<br>
disre_mixed = yes<br>
disre_tau = 10<br>
nstdisreout = 5000<br>
; dihedral restraints NMR refinement<br>
dihre = simple<br>
dihre_fc = 1000<br>
dihre_tau = 0.0<br>
nstdihreout = 5000<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>
tau_t
= 0.1 0.1<br>
tc-grps = Protein SOL<br>
ref_t
= 300 300<br>
; Pressure coupling is on<br>
Pcoupl = berendsen<br>
tau_p = 2.0<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
pcoupltype = isotropic<br>
; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
----------------------------------------------------------<br>
-----------<span style="font-weight: bold;">in my top file i have added the following lines for distance restraints, dihedral restraints, position restraints</span>.....................................<br>
<br>
[ distance_restraints ]<br>
; ai aj type index type' low up1 up2 fac<br>
; HBONDS constraints<br>
40 80 1 0 2 0.15 0.23 0.25 1.0<br>
79 40 1 1 2 0.23 0.34 0.36 1.0<br>
.....................................................<br>
...........................................................<br>
; NOE<br>
29 19 1 58 1 0.18 0.50 0.52 1.0<br>
42 19 1 59 1 0.18 0.50 0.52 1.0<br>
42 29 1 60 1 0.18 0.28 0.30 1.0<br>
.....................................................<br>
...........................................................<br>
[ dihedral_restraints ]<br>
; ai aj ak al type label phi dphi kfac power<br>
;phi<br>
7 9 11
16 1 1 -126.0
5 1 2<br>
16 18 20 26
1 1 -65.5 5
1 2<br>
26 28 30 39
1 1 -61.3 5
1 2<br>
.....................................................<br>
...........................................................<br>
; psi<br>
1 5 7
9 1 1 -49.7
5 1 2<br>
9 11 16 18
1 1 147.2 5
1 2<br>
.....................................................<br>
...........................................................<br>
; Include Position restraint file<br>
#ifdef POSRES<br>
#include "posre.itp"<br>
#endif<br>
--------------------------------<span style="font-weight: bold;">errors in pr.log</span>-------------------------------<br>
.....................................................<br>
.........................................................<br>
Max number of graph edges per atom is 4<br>
There are 130 distance restraints involving 136 atom pairs<br>
.........................................................<br>
There are 1 dihedral restraints involving 107 atom quartets<br>
.........................................................<br>
Step 122, time 0.244 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max 0.992379 (between atoms 114 and 115) rms 0.042239<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
114 115
90.0 0.1001
0.1992 0.1000<br>
Constraint error in algorithm Lincs at step 122<br>
.......................................................<br>
<br>
wating for suggestion to solve this problem.<br>
<br>
<br>
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