Dear Ross,
Thank you for your relply. I made the prmtop and inpcrd file with tleap in ambertools1.5. And I did not find the item you shown to me in my promtop files. Also, in the mdout files, it shows that sander did not find the factor in topology files, so sander used the default value. Is that caused by my low version ambertools or tleap? I will ask to the administrator whether it's possible to run xleap on HPC.
Have a good day.
Xiaoquan.
2013-08-20
egeh00
发件人：Ross Walker <ross.rosswalker.co.uk>
发送时间：2013-08-19 23:19
主题：Re: [AMBER] Question about different SCEE&SCNB to specified atom pairs.
收件人："AMBER Mailing List"<amber.ambermd.org>
抄送：
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 Tue Aug 20 2013 - 08:30:02 PDT
