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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Received on Tue Dec 20 2011 - 08:00:03 PST
