Dear David and Bill,
Thanks for your kind reply. I can able rectify the problem with leap and
structure is looking fine now, but still the system have high positive
energy during the simulation. I can't able to figure out the exact problem.
A part of the output file is given below. Please have a look and help me
*******************************************************************************************
A V E R A G E S O V E R 100000 S T E P S
NSTEP = 100000 TIME(PS) = 700.000 TEMP(K) = 299.91 PRESS =
199.9
Etot = 26758.9414 EKtot = 13635.8590 EPtot =
13123.0823
BOND = 1939.7948 ANGLE = 7047.8861 DIHED =
3285.9498
1-4 NB = 1611.8557 1-4 EEL = 58661.2231 VDWAALS =
-19144.1023
EELEC = -40279.5248 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 5957.0400 VIRIAL = 3338.8033 VOLUME =
606689.6355
Density =
0.9532
Ewald error estimate: 0.2723E-04
**************************************************************************************************
Thanks in advance
Aneesh
On Sun, May 3, 2009 at 11:30 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > Unless you actually have three-atom or four-atom rings in your
> structure..
>
> If you look at it in xleap you will see all the bonds that leap
> knows about.
>
> Bill
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 20 2009 - 14:50:09 PDT
