Adk44: Created page with "==== 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.inpcr..."

2019-05-13T12:42:01Z

Created page with "==== 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.inpcr..."

New page

==== 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.

Conversion between different data file formats - Revision history

Adk44: Created page with "==== 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.inpcr..."