Hi,
I am trying to prepare a protein for MD with amber, using for example Maestro or Chimera. This protein has a Cu+2 atom. Once I have the partial charges and hydrogens, I save the molecule in mol2 format but when I open them with tleap for solvation, etc. it seems that the mol2 file is not read properly so the atoms are not properly recognized.
For example:
(using default radius 1.500000 for CD1)
(using default radius 1.500000 for CD2)
(using default radius 1.500000 for CE1)
(using default radius 1.500000 for CE2)
(using default radius 1.500000 for OH)
(using default radius 1.500000 for CU)
I have also tried the opposite reading pdb directly, but in this case the copper atom is not recognized:
Unknown residue: CU number: 283 type: Terminal/last
And then the charge is not correct.
What is the right way to go?
Thanks a lot,
Fabian
_______________________________
Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
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Received on Mon Jun 03 2013 - 05:00:03 PDT
