Hi,
By default the 'nativecontacts' command excludes solvent. If you want
it to include solvent explicitly just specify 'includesolvent'. Hope
this helps,
-Dan
On Sat, Apr 7, 2018 at 8:09 AM, David Sáez <davidsaez.udec.cl> wrote:
> Thanks for your help, it works. And using pytraj made it much easier. But
> using cpptraj or pytraj, when I try to calculate the mindist between an
> atom and the group defined by :WAT.O, it says the selection involving the
> solvent is empty.
>
> On Thu, Apr 5, 2018 at 6:31 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Yes, via 'nativecontacts mindist'. See manual for full details.
>>
>> -Dan
>>
>> On Thu, Apr 5, 2018 at 5:13 PM, David Sáez <davidsaez.udec.cl> wrote:
>> > Dear Amber users,
>> >
>> > Years ago, I used in GROMACS a tool (mindist) that allowed, given two
>> > non-overlapping groups of atoms, the computation of the distance between
>> > the two closest members of these groups. Do you know if this same goal
>> can
>> > be achieved using cpptraj?
>> >
>> > Thanks for your help,
>> >
>> > David.
>> > _______________________________________________
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>> > AMBER.ambermd.org
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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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>>
> _______________________________________________
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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 Tue Apr 10 2018 - 07:00:04 PDT
