AMBER Archive (2009)

Subject: Re: [AMBER] ambertools for NAMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 07 2009 - 08:36:27 CDT

you need to be specific about what you mean by "amber" force field.
there are many, with different functional forms and parameters.
I worry that you get a "parm file in amber 7" message- that's pretty old.
the HW-HW are likely water.
the 10-12 terms have not been used for a long time.
so we can try to help, but are you sure this is really the force field
you want to use??

On Thu, May 7, 2009 at 8:35 AM, Jorgen Simonsen <jorgen589_at_gmail.com> wrote:
> Hi all,
>
> I am trying to run a MD simulation using NAMD but ht eamber force field but
> I get an error message when trying to run the input file
>
> 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
>
> I know that there has been a bug but it should be fixed in the NAMD 2.7b1
> version - I have looked into the *.prmtop file and I find the HW in %FLAG
> AMBER_ATOM_TYPE
> %FORMAT(20a4)
>
> section but then I don't find it anymore in any of the other sections. Any
> suggestions or hints how to solve the problem or debug the parameter file?
>
> Thanks in advance
>
> Best
> J
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