Difference between revisions of "MSUP-task7-journal"

From Bioinformatikpedia
(Minimise)
(Gromacs)
Line 36: Line 36:
 
For minimise we used a slightly adapted version of the [[Task7_Hemochromatosis_Protocol#Minimise]] shell script from the heterochromatisis group.
 
For minimise we used a slightly adapted version of the [[Task7_Hemochromatosis_Protocol#Minimise]] shell script from the heterochromatisis group.
 
== Gromacs ==
 
== Gromacs ==
  +
=== repairPDB ===
  +
  +
USAGE: repairPDB <PDB FILE> [<RANGE>] [<CHAIN:] [<CHAIN:RANGE>] [OPTIONS]
  +
OPTIONS: [-offset value] offset the residue numbering
  +
[-chain char] change Chain ID
  +
[-ratom] renumber Atoms
  +
[-rres] renumber Residues
  +
[-noh] remove hydrogens
  +
[-het] do not change HETATM to ATOM for AA
  +
[-seq] protein sequence from AA
  +
[-seqrs] protein sequence from SEQRES entries
  +
  +
[-jprot] just Protein OR
  +
[-nohoh] no water OR
  +
[-ssw cutoff] print only waters with B-value below cutoff OR
  +
[-cleansol] remove overlapping solvent for GROMACS
  +
  +
[-dna] print DNA only OR
  +
[-nodna] do not print DNA

Revision as of 11:45, 25 June 2012

Scwrl

Sequence extraction from pdb-file:

/opt/SS12-Practical/scripts/repairPDB 2bfd_A.ent -chain A -seq
sequence mutated:
kpqfpgasaefidklefiqpSvisgipiyrvIdrqgqiinpsedphlpkekvlklyksmtll
ntmdrilyesqrEgrisfymtnygegtvgsaaaldntdlvfgareagvlmyrdyplelfmaq
cygnisdlgkgrqpvygckerhfvtissplatqTpqavgaayaakrananrvvicyfgegaa
segdahagfnfaatleYpiiffcrnngyaistptseqyrgdgiaargpgygimsirvdgndv
favynaRkearrravaenqpflieTmtyrigstdhpVsrlrhylqgwwdeeqekawrkqsrr
kvmeafeqaerkpkpSpnllfsdvyqempaqlrkqqeslaHhlqtygehypldhfdk

posmap:

snp-pospdb-pos-mapping
N71SN21S
M82IM32I
Q125EQ75E
I213TI158T
C258YC203Y
T310RT255R
A328TA273T
I361VI285V
N404SN326S
R429HR351H

Commad for SCWRL4:

/opt/SS12-Practical/scwrl4/Scwrl4 -i 2bfd_A.ent -s BCKDHA_2bfd_a.sequence_final -o model_OUT.pdb

FoldX

For FoldX we used the following Files

Minimise

For minimise we used a slightly adapted version of the Task7_Hemochromatosis_Protocol#Minimise shell script from the heterochromatisis group.

Gromacs

repairPDB

USAGE: repairPDB <PDB FILE> [<RANGE>] [<CHAIN:] [<CHAIN:RANGE>] [OPTIONS] OPTIONS: [-offset value] offset the residue numbering

         [-chain char]   change Chain ID
         [-ratom]        renumber Atoms
         [-rres]         renumber Residues
         [-noh]          remove hydrogens
         [-het]          do not change HETATM to ATOM for AA
         [-seq]          protein sequence from AA
         [-seqrs]        protein sequence from SEQRES entries
         [-jprot]        just Protein OR
         [-nohoh]        no water OR
         [-ssw cutoff]   print only waters with B-value below cutoff OR
         [-cleansol]     remove overlapping solvent for GROMACS
         [-dna]          print DNA only OR
         [-nodna]        do not print DNA