AMBER Archive (2009)

Subject: RE: [AMBER] ambertools for NAMD

From: Andrew Purkiss-Trew (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Thu May 07 2009 - 10:16:40 CDT

It was certainly the case in older versions NAMD (2.4 and 2.5). The
problem wasn't the actual parameters read in, but the section of the
code that converted the Amber input files. It attempted to apply
constraints which were not present in the Amber file (the angle terms)
and complained about constraints that it didn't expect (the HW-HW
term).

You had to explicitly override the way it was setting up these
constraints and it all worked. I don't know what the current state of
play with Amber input is in NAMD, but the version that has produced the
error is clearly not happy with the HW-HW distance and I used to have
exactly the same symptoms.

Can the original poster, e-mail his NAMD input file.

On Thu, 2009-05-07 at 09:51 -0500, Wei Huang wrote:
> For NAMD, I don't think so. It depends on how you prepare the input files.
>
> In the topology file for TIP3 water, there is a line said you need to have
> H1-H2 bond if SHAKE is used.
> "!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake"
>
> Jorgen, could you tell us details about how you prepare the input files?
>
> Cheers,
> Wei
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
> Of Andrew Purkiss-Trew
> Sent: Thursday, May 07, 2009 9:30 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] ambertools for NAMD
>
> On Thu, 2009-05-07 at 10:09 -0400, David A. Case 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.
> >
> > > the HW-HW are likely water.
> >
> > I agree, and these may be treated specially in NAMD. But I'm hoping there
> are
> > NAMD users on the list who will know for sure what is going on.
> >
>
> >From memory, NAMD treats TIP3P-like water differently to Amber.
>
> Amber uses three bonds (with Shake to constraint all the distances, 2 x
> OW-HW and one HW-HW)
>
> NAMD, by default, uses the HW-OW-HW bond angle and the 2 OW-HW distances
> to do the same thing.
>
> There was a way to force Amber-like behavior, but I can't remember what
> it was off the top of my head. There should be instructions in the NAMD
> documentation, try looking for 'use of Amber force field'
>
>
>
>
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-- 
Andrew Purkiss-Trew
X-ray Laboratory
London Research Institute
Cancer Research UK

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