Re: [AMBER-Developers] TER card issue with ambpdb

From: Ilyas Yildirim <>
Date: Mon, 2 Jul 2012 17:31:27 -0500 (CDT)

Jason -

I did what you suggested and ended up with "Molecule atoms are not
contiguous!". I also followed what Dave suggested; created the
prmtop/inpcrd files after re-ordering the atoms the way Dave suggested.
That prmtop, however, did not give me this contiguous error message.

My question is what this (bad) prmtop file will do on the pressure
calculations. In both, (bad) prmtop and (right) prmtop files, I have
exactly the same ATOMS_PER_MOLECULE sections. Does that mean the pressure
calculations will be the same, as well? Or during the pressure
calculations, some other sections in prmtop files (combined with
ATOMS_PER_MOLECULE) are used? Thanks.

   Ilyas Yildirim, Ph.D.
   = Department of Chemistry - 2145 Sheridan Road =
   = Northwestern University - Evanston, IL 60208 =
   = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
   = =

On Mon, 2 Jul 2012, Jason Swails wrote:

> On Mon, Jul 2, 2012 at 5:04 PM, Ilyas Yildirim
> <>wrote:
>>> Now, if you make a link between metal1 and chain1, you get a new molecule
>>> (made up of the atoms in chain1 plus metal1) that are not contiguous
>>> in atom sequence. In this case, LEaP doesn't complain, but creates an
>>> incorrect prmtop file (with a bad ATOMS_PER_MOLECULE section.) The
>>> ambpdb program uses this information to create (bad) TER cards; but
>>> the sander/pmemd programs also use this (bad) information in computing
>>> pressures. So, the prmtop file has to be fixed.
>> Thanks for the information Dave. How bad would this (bad) prmtop affect
>> the computed pressures in sander/pmemd calculations? I have done a bunch
>> of calculations with (bad) prmtop and wonder if I should throw everything
>> out. Thanks.
> Before throwing everything out, there is a simple test to see if anything
> is blatantly *wrong*. A simple test is
> your_prmtop <<EOF
> setMolecules True
> outparm test.prmtop
> This should dump test.prmtop with a "correct" ATOMS_PER_MOLECULE section
> (and SOLVENT_POINTERS). If the ordering is messed up, you'll see a message
> like "Molecule atoms are not contiguous!". Otherwise, compare the two
> prmtops (ignoring whitespace). If
> diff -w your_prmtop test.prmtop
> returns differences, it's worth inspecting them.
> HTH,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER-Developers mailing list

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Received on Mon Jul 02 2012 - 16:00:03 PDT
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