Hi AMBER Users
I am trying to carry out QMMM driven energy minimization on a double stranded RNA sequence having 5 nucleotides on each strands. I have added explicit water molecules as well as counterions too. I am treating all the RNA residues with QM using PM3 while the other parts are treated with classical MM.
Now after doing even 199000 steps of steepest descent and 1000 steps of conjugate gradient minimization, the energy is still not stable. Kindly guide me how can I use the QMMM method to get a reliable optimized structure for my RNA sequence.
My PC configuration is --- Intel Core2 Duo; 3GB RAM.
With regards!!
Gunajyoti Das
NEH University
Shillong-22
India
ont-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;
mso-font-charset:0;
mso-generic-font-family:roman;
mso-font-pitch:variable;
mso-font-signature:-1610611985 1107304683 0 0 159 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-unhide:no;
mso-style-qformat:yes;
mso-style-parent:"";
margin:0in;
margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:10.0pt;
font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman";}
.MsoChpDefault
{mso-style-type:export-only;
mso-default-props:yes;
font-size:10.0pt;
mso-ansi-font-size:10.0pt;
mso-bidi-font-size:10.0pt;}
.page Section1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;
mso-header-margin:.5in;
mso-footer-margin:.5in;
mso-paper-source:0;}
div.Section1
{page:Section1;}
-->
The INTERNET now has a personality. YOURS! See your Yahoo! Homepage.
http://in.yahoo.com/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 18 2010 - 06:30:11 PST
