[gmx-users] Re:mdrun_problem

[pkmukher]

Hi users,

I am having a problem during the running of the mdrun
program on my prepared system.I have a system containing a
protein/peptide complex. i have prepared the protein using
the pdb2gmx utility and the peptide using the PRODRG
utility. I have then included the ligand .itp file into the
protein top file. when i run grommpp followed by mdrun I see
a translation of the peptide/protein complex  in the output
structure file(also confirmed by looking at the actual pdb
file coordinates). Tranlation of a system to a new point
(e.g. center of solvent box) is a normal procedure and would
not effect calculations because the position of the peptide
and the protein within the complex would remain the same
relative to each other. However in this case i find that a
translation of the X coordinates has been performed for the
protein atoms while a translation of the Y and Z coordinates
has been performed for the peptide. This results in the
peptide moving outside of the binding site of the protein
i.e. the protein and the peptide are not placed at the same
place "relative to each other" as present in the input
structure file.I have included portions of the input and the
output structure files.

 
 

In these files (given below)

input file
 atoms 1890-1895 - last five atoms of protein in the input
file
 atoms    1-10 - first ten atoms of the peptide in the input
file

output file

atoms 1890-1895 - last five atoms of protein in the output
file
atoms 1896-1905 - first ten atoms of the peptide in the
output file

as an example

this particular protein atom from the input file
ATOM   1890  CD2 HIS A 181      17.104 -17.966  35.020  1.00

gets translated to 

ATOM   1890  CD2 HIS A 181      57.476 -17.958  35.022  1.00

NOTE: translation in X coordinates only


while 

the first ligand atom from the input file
HETATM    1  NAA DRG   182       3.259 -11.741 -15.248  1.00


gets translated to 

ATOM   1896  NAA DRG B 182       3.259  41.631  44.612  1.00


NOTE: translated in Y and Z coodinates only.

thus the protein has been translated as [X,0,0] 
while the peptide has been translated by [0,Y,Z]

The desired translation for protein is [X,Y,Z] 
and the desired translation for the ligand is [X,Y,Z].

Could you kindly help me with your suggestions. Thanks in
advance

####
input structure
####

ATOM   1890  CD2 HIS A 181      17.104 -17.966  35.020  1.00
 0.00
ATOM   1891  CE1 HIS A 181      15.979 -16.114  34.942  1.00
 0.00
ATOM   1892  NE2 HIS A 181      17.022 -16.732  34.381  1.00
 0.00
ATOM   1893  C   HIS A 181      15.328 -21.621  37.119  1.00
 0.00
ATOM   1894  O1  HIS A 181      14.341 -22.372  36.561  1.00
 0.00
ATOM   1895  O2  HIS A 181      15.818 -21.755  38.381  1.00
 0.00
TER
HETATM    1  NAA DRG   182       3.259 -11.741 -15.248  1.00
20.00
HETATM    2  HAA DRG   182       2.868 -11.170 -15.970  1.00
20.00
HETATM    3  HAB DRG   182       4.140 -12.104 -15.551  1.00
20.00
HETATM    4  HAC DRG   182       2.637 -12.498 -15.050  1.00
20.00
HETATM    5  CAB DRG   182       3.456 -10.923 -14.017  1.00
20.00
HETATM    6  CAC DRG   182       4.054 -11.797 -12.913  1.00
20.00
HETATM    7  OAD DRG   182       3.478 -12.789 -12.512  1.00
20.00
HETATM    8  N   DRG   182       5.208 -11.438 -12.418  1.00
20.00
HETATM    9  HAD DRG   182       5.666 -10.619 -12.763  1.00
20.00
HETATM   10  CA  DRG   182       5.843 -12.248 -11.340  1.00
20.00

####
output structure
####

ATOM   1890  CD2 HIS A 181      57.476 -17.958  35.022  1.00
 0.00
ATOM   1891  CE1 HIS A 181      56.353 -16.113  34.945  1.00
 0.00
ATOM   1892  NE2 HIS A 181      57.395 -16.742  34.389  1.00
 0.00
ATOM   1893  C   HIS A 181      55.696 -21.634  37.130  1.00
 0.00
ATOM   1894  O1  HIS A 181      54.730 -22.362  36.575  1.00
 0.00
ATOM   1895  O2  HIS A 181      56.185 -21.754  38.363  1.00
 0.00
ATOM   1896  NAA DRG B 182       3.259  41.631  44.612  1.00
 0.00
ATOM   1897  HAA DRG B 182       2.868  42.201  43.887  1.00
 0.00
ATOM   1898  HAB DRG B 182       4.140  41.267  44.306  1.00
 0.00
ATOM   1899  HAC DRG B 182       2.637  40.873  44.807  1.00
 0.00
ATOM   1900  CAB DRG B 182       3.456  42.447  45.837  1.00
 0.00
ATOM   1901  CAC DRG B 182       4.052  41.573  46.943  1.00
 0.00
ATOM   1902  OAD DRG B 182       3.475  40.579  47.344  1.00
 0.00
ATOM   1903  N   DRG B 182       5.210  41.933  47.440  1.00
 0.00
ATOM   1904  HAD DRG B 182       5.668  42.752  47.095  1.00
 0.00
ATOM   1905  CA  DRG B 182       5.844  41.127  48.515  1.00
 0.00


####
.mdp file
####

cpp             = /usr/bin/cpp
constraints     = none
integrator      = cg
nsteps          = 1
emtol           = 100.0
emstep          = 0.01
nstcomm         =1
ns_type         = grid
morse           = no ; was given as yes in tutorial
coulombtype     = shift
vdw_type        = shift
rlist           = 1.4
rcoulomb        = 1.2
rvdw            = 1.2
rcoulomb_switch = 1.0
rvdw_switch     = 1.0
epsilon_r       = 6.0


   



Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi
USA

Cell   - 662 380 0146
Office - 662 915 1286