The nice part about cpptraj is that you should be able to use it the same
way you use ptraj (as long as cpptraj has that functionality).
If you wish to take advantage of what cpptraj has to offer that ptraj does
not, _then_ you will have to learn more/different stuff :).
HTH,
Jason
On Tue, Dec 20, 2011 at 10:31 AM, Jio M <jiomm.yahoo.com> wrote:
> Hi,
>
>
> I get problem in AT1.2 and also in AT1.5. But when I use -aatm flag its
> giving OK results.
>
> >>Ptraj is broken here, but cpptraj seems OK, so you might try that.
>
> main problem is that ptraj does not write correct pdb so I guess it wont
> do correct analysis. "cpptraj" is new for me, as I read from manual I have
> to explore it.
>
> thanks and regards;
> JIomm
>
> Merry Xmas to all
>
> :-)
>
>
> ________________________________
> From: David A Case <case.biomaps.rutgers.edu>
> To: Jio M <jiomm.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
> Sent: Tuesday, December 20, 2011 5:50 AM
> Subject: Re: [AMBER] problem in writing pdb with ambpdb:test case attached
>
> On Mon, Dec 19, 2011, Jio M wrote:
> >
> >
> > >>If you are using up-to-date code, please try to construct a small
> example
> > >>that illustrates the problem
> >
> > I have attached test1.libĀ (its just a fragment part of my system, so
> > please ignore overall charge) from which test1.prmtop and inpcrd were
> > generated. If ambpdb (without -aatm flag) is used it generates wrong
> > atom names in pdb file. So is with ptraj generated pdbs. So I am not
> > sure whether ptraj analysis will be correct or not. But as of case now I
> > have re-named and reduced 4 character name to 3.
>
> I am unable to reproduce the problem you see. Is there any chance that the
> ambpdb exectuable you are actually running is from an earlier version of
> AmberTools? In any event, I guess you can use the "-aatm" flag.
>
> Ptraj is broken here, but cpptraj seems OK, so you might try
> that.
>
> ...dac
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Dec 20 2011 - 21:30:03 PST
