AMBER Archive (2005)

Subject: Re[2]: AMBER: Force field modification problem

From: sychen (yuann_at_bioinfo.ndhu.edu.tw)
Date: Mon May 30 2005 - 19:05:45 CDT

Dear Prof. Case,
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...
Thanks for your help.

In leaprc.mod.rna.ff99, I replace
'loadOff all_nucleic94.lib' by 'loadOff all_nucleic94_modified.lib'
and add 'frcmod = loadamberparams OH2OT.dat'
In all_nucleic94_modified.lib, I changed O3' (in RC3) atom type from OH
to OT (because my tail base is RC3)and the content of OH2OT.dat:

MASS
OT 16.00 0.00 oxygen of O3' in RC3

BOND
CT-OT 320.00 1.410 PARM99 CT-OH
OT-HO 553.00 0.960 PARM99 OH-HO

ANGL
CT-OT-HO 55.00 108.50 PARM99 CT-OH-HO
CT-CT-OT 50.00 109.50 PARM99 CT-CT-OH
OT-CT-H1 50.00 109.50 PARM99 H1-CT-OH

DIHE
X -CT-OT-X 3 0.50 0.00 3. P99 X-CT-OH-X
OT-CT-CT-CT 9 1.40 0.00 3. based on P99
X-CT-CT-X
OT-CT-CT-OT 1 0.144 0.00 -3. parm98,
TC,PC,PAK
OT-CT-CT-OT 1 1.175 0.00 2. parm98,
TC,PC,PAK
OS-CT-CT-OT 1 0.144 0.00 -3. parm98,
TC,PC,PAK
OS-CT-CT-OT 1 1.175 0.00 2. parm98,
TC,PC,PAK
H1-CT-CT-OT 1 0.25 0.00 1. Junmei et al,
1999
HC-CT-CT-OT 1 0.25 0.00 1. Junmei et al,
1999
HO-OT-CT-CT 1 0.16 0.00 -3. Junmei et al,
1999
HO-OT-CT-CT 1 0.25 0.00 1. Junmei et al,
1999

IMPR

NONB
  OT 1.7210 0.2104 OPLS

On Mon, 30 May 2005 09:21:00 -0700
"David A. Case" <case_at_scripps.edu> wrote:

> On Mon, May 30, 2005, yuann wrote:
>
> > I've noticed one strange problem when I tried to replace
> > the current force field parameters. I'd like to simulate a
> > RNA(single strand)-ligand complex, and I defined only a new atom
> > type called OT(as OH behaves) on O3' in the tail of my single
> > strand RNA ribose in order to reproduce, such as OH-CT-CT-OH
> > defined in parm98. This is because my ligand(mainly carbohydrates)
> > contains many OH and I prefer to use Glycam force field on my ligand.
> >
> > However, I can't obtain the same 'RNA_only' topology file after such
> > modification(AMBER8/tleap). Thanks in advance for your help.
>
> I am not sure what you mean here: what exactly is the problem you have?
> I don't understand that phrase "the same ... topology file": same as what?
>
> ...regards...dac
>
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