[AMBER] AMBER-Tools cpptraj residue numbering incorrect

From: Marko Wehle <Marko.Wehle.mpikg.mpg.de>
Date: Mon, 4 Feb 2013 16:52:55 +0100

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

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 04 2013 - 08:00:05 PST
Custom Search