[gmx-users] problem during position restraint simulation

[Moutusi Manna]

Dear all, 

            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.

--------------------------------------------------------------------------------------------------------------

Polak-Ribiere Conjugate Gradients converged to Fmax < 150 in 59 steps

Potential Energy  = -4.1081506e+05

Maximum force     =  1.3278603e+02 on atom 213

Norm of force     =  1.1614658e+01



Performed 72 energy evaluations in total.

-------------------------------------------------------------------------------------------------------------

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.

------------------my pr.mdp--------------

title               =  sp position restraining

cpp                 =  /usr/bin/cpp

define              =  -DPOSRES

constraints         =  all-bonds

constraint_algorithm=  lincs

lincs_order         =  4

lincs_iter          =  1

lincs_warnangle     =  30

integrator          =  md

dt                 
=  0.002    ; ps !

nsteps              =  250000 ; total 1 ns

nstcomm             =  1

nstxout             =  1000

nstvout             =  1000

nstfout             =  0

nstlog              =  1000

nstenergy           =  1000

nstlist             =  10

ns_type             =  grid

rlist               =  0.9

rcoulomb            =  0.9

vdwtype             =  Cut-off

rvdw                =  1.2

fourierspacing      =  0.12

fourier_nx          =  0

fourier_ny          =  0

fourier_nz          =  0

coulombtype         =  PME

pme_order           =  4

ewald_rtol          =  1e-5

optimize_fft        =  yes

;distance restraints NMR refinement

disre               =  simple

disre_weighting     =  equal

disre_fc            =  1000

disre_mixed         =  yes

disre_tau           =  10

nstdisreout         =  5000

; dihedral restraints NMR refinement

dihre               =  simple

dihre_fc            =  1000

dihre_tau           =  0.0

nstdihreout         =  5000

; Berendsen temperature coupling is on in two groups

Tcoupl              =  berendsen

tau_t              
=  0.1         0.1

tc-grps             =  Protein     SOL

ref_t              
=  300         300

; Pressure coupling is on

Pcoupl              =  berendsen

tau_p               =  2.0

compressibility     =  4.5e-5

ref_p               =  1.0

pcoupltype          =  isotropic

; Generate velocites is on at 300 K.

gen_vel             =  yes

gen_temp            =  300.0

gen_seed            =  173529

----------------------------------------------------------

-----------in my top file i have added the following lines for distance restraints, dihedral restraints, position restraints......................................



[ distance_restraints ]

; ai aj type index type' low  up1  up2  fac

; HBONDS constraints

  40 80  1     0    2    0.15 0.23 0.25 1.0

  79 40  1     1    2    0.23 0.34 0.36 1.0

 .....................................................

...........................................................

; NOE

  29  19 1    58    1    0.18 0.50 0.52 1.0

  42  19 1    59    1    0.18 0.50 0.52 1.0

  42  29 1    60    1    0.18 0.28 0.30 1.0

  .....................................................


...........................................................

[ dihedral_restraints ]

; ai aj ak al type label phi dphi kfac power

;phi

 7    9    11  
16   1   1   -126.0  
5   1   2

 16   18   20   26  
1   1   -65.5    5  
1   2

 26   28   30   39  
1   1   -61.3    5  
1   2

 .....................................................



...........................................................

; psi

 1    5    7   
9    1   1   -49.7   
5   1   2

 9    11   16   18  
1   1    147.2   5  
1   2

 .....................................................




...........................................................

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

--------------------------------errors in pr.log-------------------------------

 .....................................................





.........................................................

Max number of graph edges per atom is 4

There are 130 distance restraints involving 136 atom pairs





.........................................................

There are 1 dihedral restraints involving 107 atom quartets





.........................................................

Step 122, time 0.244 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

max 0.992379 (between atoms 114 and 115) rms 0.042239

bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

    114    115  
90.0    0.1001  
0.1992      0.1000

Constraint error in algorithm Lincs at step 122





.......................................................



wating for suggestion to solve this problem.







Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090811/a39f39a4/attachment.html>