Ptraj question -- Re: AMBER: carnal problem

From: Joseph Fernandez <>
Date: Thu, 8 Sep 2005 10:04:14 -0700 (PDT)

I would like to identify the atom ID of all water
molecules that come within a distance of a set of
atoms in the solute molecule over the course of a
simulation **using ptraj**. Is there a facility in
ptraj to do this? I normally use carnal to do this
(the two pass procedure in the example section), but
if carnal will be dropped from the AMBER distribution,
it would make sense to provide this useful option in
ptraj. It used to be that the "closestwaters" option
would report actual atom IDs of water molecules, which
is no longer the case. Other than reverting to older
ptraj versions, what would be a solution to this


--- Bill Ross <> wrote:

> > I am using carnal to analyse H-bonds including
> solvent molecules. The size
> > of the molecule is 928 residues and there are
> around 27000 water
> > molecules. While running the carnal, I get the
> following error:
> >
> > "malloc 1480614768 bytes: Cannot allocate memory
> > Not enough memory: try 'limit' to see
> > if e.g. 'unlimit datasize' may help.
> > Otherwise, increasing swap space may
> > be possible"
> >
> > I have tried increasing swap space from 1GB to
> 2GB, but I get the same
> > error. I would appreciate any kind of help.
> Did you try 'limit' etc. first? Swap is probably
> irrelevant if
> limits are holding you back.
> It may be that you are simply trying to do too much
> for your
> operating system. Seeing your input file and knowing
> what
> sort of machine you are on might help.
> Carnal will be dropped from Amber due to lack of
> interest in
> supporting it, so you could also consider trying
> ptraj.
> Bill
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Received on Thu Sep 08 2005 - 18:53:00 PDT
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