Hi,
I recommend using cpptraj from AmberTools 13 (updated to the latest
version, 13.22) as it contains many bug fixes and improvements over the
ptraj code. In addition, you can perform IRED analysis in one pass with
cpptraj (see AmberTools 13 manual section 8.15.4 "The Cpptraj IRED
Approach").
-Dan
On Fri, Mar 7, 2014 at 5:31 PM, ¨v¥ß <xiaoli19871216.gmail.com> wrote:
> Hi, Dan:
> I use the ptraj of amber12.
> Thank you
> Li
>
>
> On Fri, Mar 7, 2014 at 4:26 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > Can you specify whether you were using ptraj or cpptraj, and which
> version
> > (i.e. what is the output of './update_amber --version' in your AMBERHOME
> > directory)?
> >
> > -Dan
> >
> >
> > On Fri, Mar 7, 2014 at 4:18 PM, ¨v¥ß <xiaoli19871216.gmail.com> wrote:
> >
> > > Hi,all:
> > > I type the following code to do the ired analysis:
> > >
> > > trajin mdcrd5
> > > vector v1 :1.N ired :1.H
> > > vector v2 :2.N ired :2.H
> > > ...
> > > matrix ired name matired order 2
> > > analyze matrix matired out ired.vec order vecs 468 orderparamfile
> > order.out
> > >
> > > It shows the following error message:
> > >
> > > "
> > >
> > >
> > > ANALYZE
> > > 1> ANALYZE MATRIX: Analyzing matrix matired and dumping results to
> > > ired.vec
> > > Calculating 468 eigenvectors and no thermodynamic data
> > > Calculating 468 eigenvectors and order parameters
> > > Order parameters will be written to order.out
> > >
> > > Segmentation fault (core dumped)
> > > "
> > > Can anyone tells me what's the matter and how to fix it?
> > > Thank you
> > > --
> > > Li Xiao
> > > University of California, Irvine
> > > Email: xiaoli19871216.gmail.com
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > -------------------------
> > 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)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Li Xiao
> University of California, Irvine
> Email: xiaoli19871216.gmail.com
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Mar 08 2014 - 08:30:03 PST
