Re: [AMBER] frcmod.urea

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Tue, 01 Feb 2011 16:11:34 +0100

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
>
>
>
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-- 
                            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
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Received on Tue Feb 01 2011 - 07:30:05 PST
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