Dear Amber Users and Developers,
today I've found a something concerning cpptraj (AMBER-Tools 1.5 & AMBER-Tools 12).
If I read in a rst file and convert it to a mol2 output, sometimes cpptraj renumbers the residues all to number 1 and names them to the name of the first residue.
echo "trajin "$name"_MINCoord.rst" > $name"_MDCoord.calc_rms"
echo "trajout "$name"_prmMol2.mol2 mol2 nobox" >> $name"_MDCoord.calc_rms"
echo "trajout "$name"_prmCoord.crd restart" >> $name"_MDCoord.calc_rms"
echo "go" >> $name"_MDCoord.calc_rms"
echo ptraj $name"_prmTop.prmtop" < $name"_MDCoord.calc_rms"
ptraj $name"_prmTop.prmtop" < $name"_MDCoord.calc_rms"
However, if I apply the same input to ptraj, it works correctly.
Sincerely yours
Marko
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Received on Mon Feb 04 2013 - 08:00:05 PST
