From: Cezary Czaplewski Date: Fri, 22 Dec 2017 13:40:47 +0000 (+0100) Subject: switch for respa, D aminoacids, saxs tutorial, license X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=cb36b6c35942e63325f33948c429d3ca77c85306;p=django_unres.git switch for respa, D aminoacids, saxs tutorial, license --- diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py index 5eb67fb..16d942a 100644 --- a/django_simple/todo/forms.py +++ b/django_simple/todo/forms.py @@ -254,6 +254,7 @@ class TaskForm_md_a(forms.Form): help_text='coupling to the thermal bath (Berendsen)') md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02, help_text='scaling of the friction coefficients (Langevin)') + md_respa = forms.BooleanField(required=False,initial=True,label='RESPA') md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB') boxx = forms.FloatField(label='Box X',initial=1000.0, @@ -403,6 +404,8 @@ class TaskForm_remd_a(forms.Form): # remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true') # remd_rest1file = forms.BooleanField(required=False,label='single restart file',initial='true') + md_respa = forms.BooleanField(required=False,initial=True,label='RESPA') + boxx = forms.FloatField(label='Box X',initial=1000.0, help_text='box x dimension') boxy = forms.FloatField(label='Box Y',initial=1000.0, diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py index fd7fd7c..2badbc2 100644 --- a/django_simple/todo/jobfiles.py +++ b/django_simple/todo/jobfiles.py @@ -90,7 +90,7 @@ CUTOFF=7.00000 WCORR4=0.00000""" if seq[-1]=='X': dimen3-=1 - nogly ='CDSQKIPTFNHLRWAVEYM' + nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym' seq2 = ''.join([c for c in seq if c in nogly]) dimen3=(dimen3+len(seq2))*3 diff --git a/django_simple/todo/templates/about.html b/django_simple/todo/templates/about.html index 1bc49fb..62d24d9 100644 --- a/django_simple/todo/templates/about.html +++ b/django_simple/todo/templates/about.html @@ -55,6 +55,14 @@ medium-resolution force field.
  • +A. Liwo, S. Ołdziej, C. Czaplewski, D. Kleinerman, P. Blood and H.A. +Scheraga. Implementation of molecular dynamics and its extensions with the +coarse-grained UNRES force field on massively parallel systems; towards +millisecond-scale simulations of protein structure, dynamics, and +thermodynamics. J. Chem. Theory Comput. 2010, 6, 890-909. +
    • + +
  • A. Liwo, M. Baranowski, C. Czaplewski, E. Gołaś, Y. He, D. Jagieła, P. Krupa, M. Maciejczyk, M. Makowski, M.A. Mozolewska, A. Niadzvedtski, S. Ołdziej, H.A. Scheraga, A.K. Sieradzan, R. Ślusarz, T. Wirecki, Y. Yin, @@ -79,8 +87,44 @@ Protein Structure and Dynamics. J. Chem. Inf. Model. 2017, 57, 2364–2377.
    • +
  • +A. Karczyńska, M.A. Mozolewska, P. Krupa, A. Giełdoń, A. Liwo, C. +Czaplewski.Prediction of protein structure with the coarse-grained UNRES +force field assisted by small X-ray scattering data and knowledge-based +information. +Proteins: Struct. Funct. Bioinf. 2017, CASP12 special issue DOI: 10.1002/prot.25421 +
    • + +

    +License terms of UNRES package implemented in the server +

      +
    • + This software is provided free of charge to academic users, subject to + the condition that no part of it be sold or used otherwise for + commercial purposes, including, but not limited to its incorporation + into commercial software packages, without written consent from the + authors. For permission contact Prof. H. A. Scheraga, Cornell + University. +
    • + This software package is provided on an "as is" basis. We in no way + warrant either this software or results it may produce. +
    • + Reports or publications using this software package must + contain an acknowledgment to the authors and the NIH Resource + in the form commonly used in academic research. +
    + +Third party software employed in the server + diff --git a/django_simple/todo/templates/details1.html b/django_simple/todo/templates/details1.html index eaf6ff3..7cc82df 100644 --- a/django_simple/todo/templates/details1.html +++ b/django_simple/todo/templates/details1.html @@ -194,6 +194,12 @@ Created {{ task.created_date }}
    mdpdb
    {{ task.md_mdpdb}}
    +
  • +
    RESPA
    +
    {{ task.md_respa}}
    +
    • + + {% endif %} {% if task.type == "remd" %} @@ -267,6 +273,11 @@ Created {{ task.created_date }} {% endif %} + +
  • +
    RESPA
    +
    {{ task.md_respa}}
    +
  • temperatures
    diff --git a/django_simple/todo/templates/input.html b/django_simple/todo/templates/input.html index 9189f6b..b667f4a 100644 --- a/django_simple/todo/templates/input.html +++ b/django_simple/todo/templates/input.html @@ -22,11 +22,24 @@ server).
  • Disulfide bonds are read from PDB based on SSBOND records and for multichain protein COMPND record with propers CHAIN: tokens listing all chains in the -PDB file. +PDB file. See example: +
    +COMPND   3 CHAIN: A, B, C, D;
+SSBOND   1 CYS C  107    CYS C  138
+SSBOND   2 CYS C  124    CYS C  139
+SSBOND   3 CYS C  137    CYS C  149
+SSBOND   4 CYS D  107    CYS D  138
+SSBOND   5 CYS D  124    CYS D  139
+SSBOND   6 CYS D  137    CYS D  149
+
  • A protein structure with disulfide bonds and no corresponding SSBOND records will result in clashes and a very high energy which can crash calculations.
  • TER records in PDB file are read to recognize chain's ends. +
  • +Distance distribution (from SAXS experiment) cam be added for MREMD +simulations in advanced mode. First column distance, second column +distribution function value (separated by space). {% endblock %} diff --git a/django_simple/todo/templates/tutorial.html b/django_simple/todo/templates/tutorial.html index d59175c..6e9bbde 100644 --- a/django_simple/todo/templates/tutorial.html +++ b/django_simple/todo/templates/tutorial.html @@ -122,7 +122,7 @@ of temperature are shown. Replica exchanges are analyzed.

    Finally cluster analysis is performed to select 5 families of conformations, and representative model from each family is converted to all-atom -and refined. +and refined. PDB files can be downloaded by clicking on the picture.

    @@ -138,6 +138,60 @@ dissulfide bonds, MD simulations of 1L2Y starting from extended chain and replica exchange simulations of 1E0G starting form extended chain using new UNRES force field and Berendsen thermostat. +

    +

  • +Distance distribution restrained (simulated SAXS data) +replica exchange molecular dynamics of +Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain. +
    +(Use Load example SAXS data button in advanced mode) +

    • +
    +
    + Show + + +
    + +