On Fri, Sep 10, 2010 at 2:26 PM, Hoshin Kim <85hskim.gmail.com> wrote:
> Dear, Amber user
>
> I am trying to do calculation of h-bond between solvent and solute. But I
> am
> having a hard to use residue mask of solvent. Because my solvent residue
> name doesn't consist of characteristic(like WAT) but number.
> My solvent is ionic liquid which is composed of 144 cation and 144 anion.
> Total 288 molecules are composed of solvent. But in case of cation, residue
> name is 111 and anion is 222. I'd like to mask N atom on all of the cation.
>
If your solvent molecules have numeric names, then you will have to specify
the solvent molecules via their residue number. For instance, if your
solvent is residues 144 to 432, or something, then use the following mask:
:144-432.N
Good luck!
Jason
So when I used :111.N, PTRAJ understand just N atom on residue number 111
> not N atoms on all of cation.
> There are too many molecules to input manually and all of cation and anion
> are randomly named their number.
> Does anyone have an idea to select only all of cation?
>
> Thanks in advance
>
> Hoshin Kim,
>
>
> ----------------------------------------------------------------------------
> -------
> Hoshin Kim
> Now)
> Visiting Scholar
> Department of Chemical and Biomolecular Engineering
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-986-9258
> Also)
> Graduate student (M.D. candidate)
> Ionic Liquids Team(ILs) in Bio Nano Process Lab
> Department of Biological Engineering,
> 2S 113, Engineering building Inha University,
> 253 Yonghyeon Dong, Nam Ku
> Incheon, KOREA
> TEL) +82-32-860-8655
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Sep 10 2010 - 12:00:04 PDT
