Difference between revisions of "Conversion between different data file formats"
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import>Csw34 |
import>Csw34 |
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cat tmp1 tmp2 > input.crd |
cat tmp1 tmp2 > input.crd |
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rm tmp1 tmp2 |
rm tmp1 tmp2 |
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| + | |||
| + | Note: for [[CHARMM]], conversion between crd and pdb can be done by CHARMM itself using an appropriate input file. More info can be found on the CHARMM page for [[ |
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Revision as of 09:21, 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: for CHARMM, conversion between crd and pdb can be done by CHARMM itself using an appropriate input file. More info can be found on the CHARMM page for [[