AMBER Archive (2009)

Subject: [AMBER] AMBER: Problems in solvation with xleap

From: vallespardojl_at_chem.leidenuniv.nl
Date: Wed Jan 07 2009 - 07:39:56 CST

Hi!

I have AMBER8 and I'm using xleap in order to solvate a molecule. I
follow all the steps of the tutorial B4 (sustiva tutorial), and seems
that all is OK, but when I try to save the topology and coordinates
file (.prmtop & .inpcrd) with the command "saveamberparm" appears the
next

Building topology.
Building atom parameters.
For atom: .R<WAT 2>.A<O 1> Could not find type: OW
For atom: .R<WAT 2>.A<H1 2> Could not find type: HW
For atom: .R<WAT 2>.A<H2 3> Could not find type: HW
For atom: .R<WAT 3>.A<O 1> Could not find type: OW
For atom: .R<WAT 3>.A<H1 2> Could not find type: HW
For atom: .R<WAT 3>.A<H2 3> Could not find type: HW
For atom: .R<WAT 4>.A<O 1> Could not find type: OW
For atom: .R<WAT 4>.A<H1 2> Could not find type: HW
For atom: .R<WAT 4>.A<H2 3> Could not find type: HW
...
For atom: .R<WAT 944>.A<O 1> Could not find type: OW
For atom: .R<WAT 944>.A<H1 2> Could not find type: HW
For atom: .R<WAT 944>.A<H2 3> Could not find type: HW
For atom: .R<WAT 945>.A<O 1> Could not find type: OW
For atom: .R<WAT 945>.A<H1 2> Could not find type: HW
For atom: .R<WAT 945>.A<H2 3> Could not find type: HW
Parameter file was not saved.

And, if I check this to files, they are empty.
I'm using leaprc.ff99 and leaprc.gaff, like in the sustiva tutorial.
And I need this topology file for a QM/MM simulation with CPMD.

Thanks a lot for the help!

Jose Luis

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