Hi Xiaoquan,
A few questions:
1) Did you use Xleap from AMBERTools 13? - this is required.
2) If you check your prmtop file are there sections entitled:
%FLAG SCEE_SCALE_FACTOR
%FORMAT(5E16.8)
and
%FLAG SCNB_SCALE_FACTOR
%FORMAT(5E16.8)
3) in your mdout files (I am also assuming you used sander, pmemd or
pmemd.cuda from AMBER 12) contain the text:
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
If not then something is wrong and for some reason the SCEE and SCNB
definitions did not get picked up correctly.
All the best
Ross
On 8/19/13 9:45 PM, "egeh00" <egeh00.aol.com> wrote:
>Dear all,
>
>I posted the similar question several days ago, I got the answer that I
>can add some information in frcmod or dat file such as the following
>example.
>CJ-CG-CJ-CJ 1 -0.04 0.0 -3 SCEE=1.0
>SCNB=1.0
> 1 -0.68 0.0 -2 SCEE=1.0
>SCNB=1.0
> 1 -0.21 0.0 1 SCEE=1.0
>SCNB=1.0
>But when I set up the parameter, I cannot find difference among the
>output files, even I set SCEE=10 and SCNB=10. Did I made something wrong?
>I did not set the SCEE and SCNB in the input files.
>
>Additionally, my water box diffused, I don't know why. I have set up the
>ntd=1 and added some PBC information in inpcrd file. Does anyone can give
>me a input file sample for a PBC system?
>
>Sincerely,
>
>Xiaoquan Sun.
>
>2013-08-19
>
>
>
>egeh00
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Received on Mon Aug 19 2013 - 21:30:03 PDT
