AMBER Archive (2008)

Subject: Re: AMBER: GBSA SA calculation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed May 07 2008 - 17:05:26 CDT

the patches are ready for amber9 and 10, we had some problems
that we couldn't readily resolve with PME though so they will
need to be stripped. I ran more tests today and will get them
sent tomorrow.

I agree that the nobox thing is a typical problem, not sure but we could
try to check for that. ore likely in this case it was that the trajin file
isn't opened unless ntwx>0 (since it is the -x file); this is fixed in the
patch.
carlos

On Wed, May 7, 2008 at 5:17 PM, David A. Case <case_at_scripps.edu> wrote:
> On Wed, May 07, 2008, Titus, Jamie (bairdje) wrote:
> >
> >
> > I am currently trying to extract SA terms from a trajectory which I have
> > stripped of H2O and ions,
>
> Did you use the "nobox" parameter in the trajout command when you stripped the
> waters and ions? Forgetting to do this is the most common cause of problems:
> your trajectory may have box information that the trajene code is not
> expecting.
>
> Of course, if you *did* use nobox, then the problem is probably somewhere
> else. A good test is to use ptraj to read in and analyze some feature, using
> your stripped trajectory and the new prmtop file, to make sure they are
> compatible with each other.
>
> (Carlos: are we getting closer to having a patch for trajene that incorporates
> Dan's changes?)
>
> ...good luck...dac
>
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