Difference between revisions of "Conversion between different data file formats"

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import>Csw34
import>Em427
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Note: conversion between .crd and .pdb can be done by [[CHARMM]]- more info can be found on the page for [[converting between '.crd' and '.pdb']]
  
Note: conversion between .crd and .pdb can be done by [[CHARMM]]- more info can be found on the page for [[converting between '.crd' and '.pdb']]
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The same thing can be done by VMD - both for AMBER and CHARMM files.

Revision as of 11:02, 1 May 2008

For AMBER

xyz -> inpcrd 

  awk '{printf("%.7f %.7f %.7f "), $1, $2, $3} {getline} {printf("%.7f %.7f %.7f\n"), $1, $2, $3}' input.xyz > input.inpcrd

For AMBER and CHARMM

crd -> pdb 

  tail +2 input.crd > tmp
  awk '{printf"%4s%7d %-4s %4s%5d%12.3f%8.3f%8.3f\n", "ATOM",$1,$4,$3,$2,$5,$6,$7}' tmp > input.pdb
  rm tmp

pdb -> crd 

  awk '{if ($1!="TER" && $1!="END") printf"%5d%5d%4s  %-4s%17.12f%17.12f%17.12f%6s  %-4d\n", $2,$5,$4,$3,$6,$7,$8,"NAME",$5}' input.pdb > tmp1
  wc -l tmp1 | awk '{print $1}'> tmp2
  cat tmp1 tmp2 > input.crd
  rm tmp1 tmp2

Note: conversion between .crd and .pdb can be done by CHARMM- more info can be found on the page for converting between '.crd' and '.pdb'

The same thing can be done by VMD - both for AMBER and CHARMM files.

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