[gmx-users] Re:mdrun_problem
Erik Marklund
erikm at xray.bmc.uu.se
Tue Aug 7 08:58:02 CEST 2007
As has been suggested already, this is probably related to PBC, and
is in fact not a problem at all. Have you checked whether applying
the PBC puts the protein and peptide back together? Try out trjconv -
ur compact on your system and have a look at the output structure, or
run g_mindist to see whether they really drift apart.
/Erik
6 aug 2007 kl. 23.18 skrev 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
>
>
>
>
>
>
>
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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