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 - 06:00:06 PST
