AMBER Archive (2009)

Subject: Re: [AMBER] catenan simulation problems

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Mar 18 2009 - 06:47:32 CDT

On Fri, Mar 06, 2009, Cristina Sisu wrote:

Sorry to be so slow in getting back on this one.

>
> I created the pdb file using $AMBERHOME/exe/ambpdb -p cat.prmtop <
> cat.inpcrd > cat.pdb .
> In antechmber I used similar commands as the ones presented in the
> antechamber tutorial, but the list is:
>
> $AMBERHOME/exe/antechamber -i cat1.pdb -fi pdb -o cat1.mol2 -fo mol2 -c
> bcc -s 2
>
> $AMBERHOME/exe/parmchk -i cat1.mol2 -f mol2 -o cat1.frcmod
>
> And in leap , i've used leaprc.ff99SB:
>
> source leaprc.gaff
> x = loadmol2 cat1.mol2
> loadamberparams cat11.frcmod
> solvateoct x TIP3PBOX 12.0
> saveamberparm x cat_wat.prmtop cat_wat.inpcrd

The problem is not with ambpdb, but with the prmtop file that LEaP
creates. If you look at the ATOMS_PER_MOLECULE section of your prmtop,
you will see that the first molecule has 92 atoms, exactly half of what
it should be. Ambpdb uses this information to make the pdb file;
fortunately, sander/pmemd does not use this for energy, although it is
used in the computation of the virial.

However, I don't see any error in the input files, and it looks like a
bug in tleap/xleap. Maybe someone on the list will recognize this
symptom. When I use sleap, I get the proper number of atoms
per molecule.

So, my best suggestion for a workaround right now is to rerun the above
commands in sleap. You should check that a single-point energy (from
some structure) is the same with the new and old prmtop files. (Be sure
to use the same input coordinates for both calcs -- tleap and sleap
appear to add the same number of water molecules, but the coordinates
might not be exactly the same.)

...hope this helps...dac

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