Hi,
On Wed, Mar 26, 2014 at 2:34 AM, Setyanto Md <stwahyudi.md.gmail.com> wrote:
>
> I'd like to know how to update my cpptraj.
>
Cpptraj is updated as part of AmberTools. To update AmberTools you need to
re-run configure, say yes to applying any patches, then re-compile like so:
cd $AMBERHOME
./configure <your configure flags>
make install
I got this from tutorial, but this mask was used with ptraj.
>
> Would somebody help me how to set up donor and acceptor mask like above ?
>
As stated in the AmberTools manual, the 'hbond' command in cpptraj is very
different from that in cpptraj. In cpptraj there is no need to define
donors and acceptors in separate commands (also note that in cpptraj,
hydrogen bond donors are defined as bound to hydrogen, which is the
opposite of ptraj). In the cpptraj 'hbond' command you can specify a single
mask and potential donors/acceptors will be searched for using F, O, and N
atoms by default. You can also specify donors and acceptors with the
'donormask' and 'acceptormask' keywords. See the manual for full details.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Mar 26 2014 - 08:00:03 PDT
