Greetings all,
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.
Sincerely,
sychen.
###new leaprc.rna.ff98
loadOff all_nucleic94_modified.lib
#my tail base is RC3, so I changed O3' atom type from OH to OT
#in all_nucleic94_modified.lib
frcmod = loadamberparams OH2OT.dat
###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
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Received on Mon May 30 2005 - 12:53:01 PDT
