Hi All,
I have a pdb file of a Zn complex for which I want to generate Amber inpcrd/prmtop files. I used antechamber and parmchk to generate mol2 and frcmod files to be used with leap. However, leap fails to read the mol2 file which antechamber generates. It is my understanding that leap should be able to load any mol2 file which has been generated by antechamber.
This is what I did:
antechamber -i zn-complex.pdb -fi pdb -o zn-complex.mol2 -fo mol2 -c bcc -s 2
parmchk -i zn-complex.mol2 -f mol2 -o zn-complex.frcmod
tleap
> source leaprc.gaff
> mod = loadAmberParams zn-complex.frcmod
> foo = loadMol2 zn-complex.mol2
Loading Mol2 file: ./zn-complex.mol2
Reading MOLECULE named 52 49 1 0 0
Fatal Error: last line read: 1 N -0.3780 1.8940 -1.9700 n3 1 -0.856800
Same happens in xleap.
Input, output and log files can be found at
http://www.wmd-lab.org/agoetz/acmol2problem
Can someone who knows antechamber and leap have a look at why this is not working?
Thanks for any help.
All the best,
Andy
--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Tue Jul 27 2010 - 18:30:03 PDT
