Dear Amber Users and Developers,
I'm sorry, this is a bit of a confusion...
cpptraj works with mol2 files... ptraj of course does not output mol2 files anyway.
It got mixed up in my script and the error occurs in tleap, while reading the cpptraj produced mol2 file and write another one out from tleap.
That one had the same name and thats why it got mixed up.
The problem is actually: if tleap reads the unprocessed mol2 files it works well, but not if it uses the one that is the output of cpptraj.
An error originates from here:
.<TRIPOS>MOLECULE
Cpptraj generated mol2 file.
20922 20850 1 0 0
Because from the cpptraj output, as it has a wrong number/count of resdiues in it's metainfo, e.g. it shows a 1 here, instead of the correct number of residues.
But this wrong count of residues occurs in both cpptraj versions of Amber-Tools 1.5 and Amber-Tools 12.
Sincerely yours,
Marko
-----Ursprüngliche Nachricht-----
Von: Marko Wehle
Gesendet: Mo 04.02.2013 16:52
An: amber.ambermd.org
Betreff: AMBER-Tools cpptraj residue numbering incorrect
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 - 11:30:02 PST
