Try changing the line
0-C-N 60.00 121.4
to
O-C-N 60.00 121.4
As for the second column in NONB, I recommend that you read the file
format description of the amber files in the manual.
On 2/1/11 4:07 PM, subrata paul wrote:
> I want to simulate urea and water using duffy model for urea. Now i want to
> make urea molecule considering following prameter...
>
> vdw parameters for URE
>
> MASS
>
> C 12.
>
> O 16.
>
> N 14.
>
> H 1.00
>
> BOND
>
> C-O 501.0 1.265
>
> C-N 448.7 1.350
>
> N-H 446.9 1.000
>
> ANGL
>
> 0-C-N 60.00 121.4
>
> N-C-N 60.04 117.2
>
> C-N-H 34.88 120.0
>
> H-N-H 39.81 120.0
>
> NONBON
>
> C 2.1043 0.1050
>
> O 1.6610 0.2100
>
> N 1.8237 0.1700
>
> H 0.0000 0.0000
> this my frcmod.urea file , is this file OK ?
> In the NONBON list What is represent by the 2nd coulmb?
>
> Using this file may i creat urea molecule? or prep file needed?
> whem i put flowing command in
> xleap -f leaprc.ff03
> UMY=loadamberparams frcmod.urea
>
> it give at the end
> UNKNOWN KEYWORD:in the parameter file
>
> Why is it coming?
>
> please help me
>
> thanking u
> subrata
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
Senior Editor. Journal of Physical Chemistry.
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 01 2011 - 07:30:05 PST
