sumanth kumar wrote:
Dear Bruce D.Ray...
I had used the TPO parameters as u gave in previous posts.
[ *TPO* ]
[ atoms ]
N *opls*_238 -0.500 1
H *opls*_241 0.300 1
CA *opls*_224B 0.140 1
HA *opls*_140 0.060 1
CB *opls*_158 0.205 2
HB *opls*_140 0.060 2
OG1 *opls*_447 -0.700 2
P *opls*_445 1.795 3
O1P *opls*_446 -1.120 3
O2P *opls*_446 -1.120 3
O3P *opls*_446 -1.120 3
CG2 *opls*_135 -0.180 4
HG21 *opls*_140 0.060 4
HG22 *opls*_140 0.060 4
HG23 *opls*_140 0.060 4
C *opls*_235 0.500 5
O *opls*_236 -0.500 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB OG1
CB CG2
OG1 P
O1P P
O2P P
O3P P
CG2 HG21
CG2 HG22
CG2 HG23
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB OG1 dih_SER_THR_chi1_N_C_C_O
C CA CB OG1 dih_SER_THR_chi1_CO_C_C_O
CA CB OG1 HG1 dih_SER_THR_chi2_C_C_OH_HO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
And i added Ryckaert-Belleman dihedrals in ffoplsaabon.itp file basing
on the errors got after i run pdb2gmx command.
And i had left the 6 coefficients (c0 to c5) as 0.0000 because i dunno
how to derive those values.
So please help me how to fill those values. I had gone through the RB
dihedrals main article but im not clear.
The fitting procedures are described in great detail in both of the OPLS papers
(Jorgensen JACS 1996 and Kaminski J Phys Chem B 2001). If there is a specific
point or technique that you're not familiar with, you'll have better luck asking
a very specific question rather than "I don't know how to do it, someone tell me
how."
-Justin
Just give me sugggestions to derive those values and if u have those
values it would me much more easier for me....:-)
Thank you in advance
sumanth
--
*SUMANTH KUMAR.M*
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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