Re: [AMBER] Fw: Problems to calculate frequencies

From: David A Case <>
Date: Thu, 25 Aug 2016 09:40:56 -0400

On Thu, Aug 25, 2016, Stregone wrote:
> molecule m;
> int ier;
> float m_xyz[dynamic], f_xyz[dynamic];
> float dgrad, fret;
> m = getpdb("new.pdb");
> allocate m_xyz[3*m.natoms];
> allocate f_xyz[3*m.natoms];
> readparm(m, "box.prmtop");

The name of the file, and the error message reported below, suggest that
the prmtop file is for a periodic simulation. NAB (and particularly its
normal mode capability) is designed for non-periodic simulations.
> Error: gb>0 is incompatible with periodic boundary conditions.

> The pdf file that I am using already comes from a minimisation (sander),
> it means that prmtop file is working. The manual says that if one has
> problems with the prmtop file, one could create a new in leap. Therefore
> I did try to create the prmtop by the following script:
> tleap -f leaprc.ff12SB -f act
> act
> > source leaprc.gaff
> loadamberparams broben.frcmod
> dibr = loadpdb new.pdb
> check dibr
> saveamberparm dibr box.prmtop box.inpcrd
> quit

Your "new.pdb" file looks like it has a non-standard residue ("BBZ"); you
need to load an amber library file that has that residue. The relevent error
in the leap.log file is this:

Unknown residue: BBZ number: 1 type: Terminal/last

You probably need to follow the procedure you used to create the periodic
prmtop file, but leave out the steps that create the periodic box. Basically,
you would have to add a command like "loadMol2 BBZ.mol2" to the commands
listed above.

...good luck...dac

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Received on Thu Aug 25 2016 - 07:00:03 PDT
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