From the Amber manual, cpptraj section, pairwise:
"The cuteelc and cutevdw keywords can be used to restrict printing of
individual interactions to those for which the absolute value is above
a cutoff."
It is likely that the missing interactions have energies less than the
default cutoffs (both 1.0 kcal/mol). Set them to 0.0 if you want all
interactions.
-Dan
On Wed, May 3, 2017 at 9:30 PM, David Case <david.case.rutgers.edu> wrote:
> On Mon, May 01, 2017, 张壮壮 wrote:
>
>> These are all files I used in my calculate. And my original purpose is
>> to get atom-atom interactions in RNA.
>
> It doesn't look like the problem has anything to do with LEaP, but rather with
> cpptraj. I'm replying with a new subject line, since the people that
> understand cpptraj probably never read your post. I agree that your
> question appears reasonable, but I've never used this option in cpptraj.
>
> ....dac
>
>> zhangzhuangzhuang
>> (lanzhou university)
>>
>> > -----Original Message-----
>> > From: 张壮壮 [mailto:zhangzhzh16.lzu.edu.cn]
>> > Sent: Wednesday, April 26, 2017 9:20 AM
>> > To: amber.ambermd.org
>> > Subject: [AMBER] consult about LEaP in amber
>> >
>> > Hello,
>> > I use LEaP to calculate atom-atom interactions energy in RNA.The platform is: Amber14 + AmberTool16. the pdb file and tleap.in and result file are attached.
>> > however.some atom-atom interactions are missed.like atom 197 with atom
>> > 240 in the 1.eout. I want to konw is this a normal or I did some wrong
>> > in some parameters?
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri May 05 2017 - 12:00:03 PDT
