AMBER Archive (2005)

Subject: Re: AMBER: Force field modification problem

From: David A. Case (case_at_scripps.edu)
Date: Tue May 31 2005 - 00:17:06 CDT

On Tue, May 31, 2005, sychen wrote:

> The original topology file for RNA_only is obtained as follows,
> tleap -f leaprc.rna.ff99
> rna = loadpdb rna.pdb
> solvatebox rna TIP3PBOX 10
> addions rna Na+ 0
> saveamberparm rna rna.org.top rna.org.crd
>
> tleap -f leaprc.mod.rna.ff99
> rna = loadpdb rna.pdb
> solvatebox rna TIP3PBOX 10
> addions rna Na+ 0
> saveamberparm rna rna.mod.top rna.mod.crd
>
> I'd like to reproduce rna.org.top by rna.mod.top except for
> the difference type name. However, there are some difference
> value between two topology files, such as difference values in
> FLAG BOND_FORCE_CONSTANT, FLAG ANGLE_FORCE_CONSTANT,
> FLAG ANGLE_EQUIL_VALUE, FLAG DIHEDRAL_FORCE_CONSTANT,
> FLAG DIHEDRAL_PHASE,... etc.
> However, The OT modification simply adopts what describe OH in Parm99...

You can use the rdparm program to print out the details of what is in your
prmtop files. It is possible that only the order of terms has changed, which
will make the prmtop files look different. You can also take a single
conformation and compute its enegy with both prmtop files. This should help
you isolate which terms are different.

The sort of test you are making is indeed an important and appropriate one to
make.

...good luck....dac

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