Difference between revisions of "Conversion between different data file formats"
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import>Em427 |
import>Msb50 |
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| + | ==== For [[AMBER]] ==== |
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| + | |||
xyz -> inpcrd |
xyz -> inpcrd |
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| − | awk '{printf("%.7f %.7f %.7f "), $1, $2, $3} {getline} {printf("%.7f %.7f %.7f\n"), $1, $2, $3}' input.xyz > input.inpcrd |
+ | awk '{printf("%12.7f %11.7f %11.7f "), $1, $2, $3} {getline} {printf("%11.7f %11.7f %11.7f\n"), $1, $2, $3}' input.xyz > input.inpcrd |
| − | |||
| + | ==== For [[AMBER]] and [[CHARMM]] ==== |
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crd -> pdb |
crd -> pdb |
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| − | tail +2 input.crd > |
+ | tail +2 input.crd > tmp |
| − | awk '{printf"%4s%7d %-4s |
+ | awk '{printf"%4s%7d %-4s%4s %s%5d%11.3f%8.3f%8.3f\n", "ATOM",$1,$4,$3,"A",$2,$5,$6,$7}' tmp > input.pdb |
| − | rm |
+ | rm tmp |
| − | |||
pdb -> crd |
pdb -> crd |
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| − | awk '{if ($1!="TER" && $1!="END") printf"%5d%5d%4s %-4s%17.12f%17.12f%17.12f%6s %-4d\n", $2, |
+ | 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 |
wc -l tmp1 | awk '{print $1}'> tmp2 |
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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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| + | |||
| + | Notes: |
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| + | |||
| + | 1. 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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| + | |||
| + | 2. The same thing can be done by [[VMD]] - both for [[AMBER]] and [[CHARMM]] files. |
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| + | |||
| + | 3. In [[AMBER]] package you can find useful program called ''ambpdb''. It can convert many formats and binary output files as well as add some interesting information like hydrogen bonds or salt bridges. |
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Latest revision as of 17:24, 7 October 2008
For AMBER
xyz -> inpcrd
awk '{printf("%12.7f %11.7f %11.7f "), $1, $2, $3} {getline} {printf("%11.7f %11.7f %11.7f\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 %s%5d%11.3f%8.3f%8.3f\n", "ATOM",$1,$4,$3,"A",$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
Notes:
1. Conversion between .crd and .pdb can be done by CHARMM- more info can be found on the page for converting between '.crd' and '.pdb'
2. The same thing can be done by VMD - both for AMBER and CHARMM files.
3. In AMBER package you can find useful program called ambpdb. It can convert many formats and binary output files as well as add some interesting information like hydrogen bonds or salt bridges.