From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 07 2009 - 07:47:07 CDT
On Thu, May 7, 2009 at 7:17 AM, Jorgen Simonsen <jorgen589_at_gmail.com> wrote:
> Hi all,
>
> I am running the NAMD version 2.6 but get a bug which should have been fix
> in version 2.5b3
>
> Reading parm file (fr.prmtop) ...
> PARM file in AMBER 7 format
> Warning: Encounter 10-12 H-bond term
> Warning: Found 350 H-H bonds.
> FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND HW - HW IN PARAMETER FILES
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND HW - HW IN
> PARAMETER FILES
>
> Charm++ fatal error:
> FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND HW - HW IN PARAMETER FILES
>
> Abort
>
> Any help to fix this or hint to debug the problem appreciated
jorgen,
are you using the right settings to make the water rigid?
amber uses an HW-HW bond to make waters rigid, while in
CHARMM style topologies you have the HW-OW-HW angle.
so while an HW-HW bond is in the topology, it should in theory
be ignored, iff the water is rigid.
on second thought, the parameters should be in your parmtop file.
i assume your input works with amber?
cheers,
axel.
>
> thanks in advance
>
> Best
> J
>
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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