Difference between revisions of "MSUP-task7-journal"
From Bioinformatikpedia
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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. |
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== Gromacs == |
== Gromacs == |
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+ | === repairPDB === |
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+ | |||
+ | USAGE: repairPDB <PDB FILE> [<RANGE>] [<CHAIN:] [<CHAIN:RANGE>] [OPTIONS] |
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+ | OPTIONS: [-offset value] offset the residue numbering |
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+ | [-chain char] change Chain ID |
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+ | [-ratom] renumber Atoms |
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+ | [-rres] renumber Residues |
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+ | [-noh] remove hydrogens |
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+ | [-het] do not change HETATM to ATOM for AA |
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+ | [-seq] protein sequence from AA |
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+ | [-seqrs] protein sequence from SEQRES entries |
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+ | |||
+ | [-jprot] just Protein OR |
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+ | [-nohoh] no water OR |
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+ | [-ssw cutoff] print only waters with B-value below cutoff OR |
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+ | [-cleansol] remove overlapping solvent for GROMACS |
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+ | |||
+ | [-dna] print DNA only OR |
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+ | [-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-pos | pdb-pos-mapping |
N71S | N21S |
M82I | M32I |
Q125E | Q75E |
I213T | I158T |
C258Y | C203Y |
T310R | T255R |
A328T | A273T |
I361V | I285V |
N404S | N326S |
R429H | R351H |
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