AMBER Archive (2009)

Subject: Re: [AMBER] ambertools for NAMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 07 2009 - 09:23:25 CDT

On Thu, May 7, 2009 at 10:09 AM, David A. Case <case_at_biomaps.rutgers.edu> wrote:
> On Thu, May 07, 2009, Carlos Simmerling wrote:
>
>> I worry that you get a "parm file in amber 7" message- that's pretty old.
>
> Believe it or not, we introduced the "new" prmtop format way back in Amber 7.
> So, when VMD says "parm7", it means "parm7 or later", as opposed to the "old",
> Amber6-and-earlier, prmtop format.
>

ah, time flies.... thanks for reminding me!
but still, since it says 10-12 are present it may be worth thinking
about whether this is a "current" model.

I'm not a NAMD expert, but I don't understand why the prmtop has bonds
between HW-HW atom types, which presumably point to the correct
parameters in the bond type list, but then NAMD says "CAN'T FIND BOND
PARAMETERS FOR BOND HW - HW IN PARAMETER FILES". shouldn't it be
there? I don't see why this would differ from other bond types.

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber