[gmx-users] LINCS warning in Position Restraint

[pandey at bioinfo.ernet.in]

Hi all,

I am trying to position restraint on 1OMB.pdb using gromacs 3.2 I have
included 2 CL- ion. My *.top is after editing:
----------------------------
[ molecules ]
; Compound        #mols
Protein             1
SOL              1768
CL-                 2
----------------------------

Am doing 5000 step of minimization (em.mdp is included below). It has
converged after 3143 steps.

I have used -posrefc 1000 while pdb2gmx. The pdb2gmx is making all the
disulfide bonds using connect statement in the pdb file.

While doing position restraint, am getting error like (below pasted) and
mdrun is getting terminated.

--------------------------------------------------------------
starting mdrun 'OMEGA-AGA-IVB (NMR, MINIMIZED AVERAGE STRUCTURE) in water'
50000 steps,     50.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.000000 (between atoms 1 and 2) rms nan
bonds that rotated more than 35 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2#
Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#
................
................
step 0
MPI: On host krypton, Program /usr/local/gromacs/bin/mdrun_mpi, Rank 6,
Process
5780 received signal SIGSEGV(11)
MPI: --------stack traceback-------
sh: line 1: idb: command not found
MPI: -----stack traceback ends-----
MPI: On host krypton, Program /usr/local/gromacs/bin/mdrun_mpi, Rank 6,
Process
5780: Dumping core on signal SIGSEGV(11) into directory
/vol1/people/student1/om
/lyso/1OMB_np_gromacs_4/test
MPI: MPI_COMM_WORLD rank 6 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 11
---------------------------------------------------------

There was 1 warning during grompp run though.
--------------------------------------------------------
Warning: atom names in
/vol1/people/student1/om/lyso/1OMB_np_gromacs_4/test/pdb.
top and /vol1/people/student1/om/lyso/1OMB_np_gromacs_4/test/pdb_b4pr.gro
don't match (CL - HW2)
.........
WARNING 1 [file
"/vol1/people/student1/om/lyso/1OMB_np_gromacs_4/test/pdb.top",
line 2147]:
  4933 non-matching atom names
  atom names from
  /vol1/people/student1/om/lyso/1OMB_np_gromacs_4/test/pdb.top will be used
  atom names from
  /vol1/people/student1/om/lyso/1OMB_np_gromacs_4/test/pdb_b4pr.gro will be
  ignored
................
renumbering atomtypes...
converting bonded parameters...
#  G96ANGLES:   493
#      PDIHS:   196
#      IDIHS:   154
#       LJ14:   573
#     POSRES:   257
#     CONSTR:   339
#     SETTLE:   1768
-----------------------------------------

I do not have any idea why this is happening?

Any help will be greatly appreciated

Thanks and Regards
Om Prakash
Bioinformatics Center
University of Pune
Pune -411007
India
-------------------------------------
em.mdp
---------------------------------------
cpp                 =  /usr/bin/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  100000
;nstcgsteep          =  1000
;
;       Energy minimizing stuff
;
emtol               =  100
emstep              =  0.01
nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
coulombtype         =  PME
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
------------------------------
pr.mdp
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
constraint_algorithm = lincs
unconstrained_start  = yes
lincs_warnangle      = 35
integrator          =  md
dt                  =  0.001    ; ps !
nsteps              =  50000    ; total 10 ps.
nstcomm             =  1
comm_mode           =  Linear
comm_grps           =  Protein  SOL     CL-
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
coulombtype         =  PME
rvdw                =  1.0
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
pbc                 =  xyz
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein  SOL     CL-
tau_t               =  0.1      0.1     0.1
ref_t               =  300      300     300
; Energy monitoring
energygrps          =  Protein  SOL     CL-
; Pressure coupling is on
Pcoupl              =  berendsen
pcoupltype          =  isotropic
tau_p               =  5        5       5       0       0       0
compressibility     =  4.5e-5   4.5e-5  4.5e-5  4.5e-5  4.5e-5  4.5e-5
ref_p               =  1.0      1.0     1.0     0       0       0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
------------------------------------