On Wed, Feb 4, 2015 at 9:55 AM, 新生大侠 <390155909.qq.com> wrote:
> Dear David:
> Thank you very much for replying my email, under your help, I fixed the
> problem I showed. you are right about the "modern" and "old" problem, after
> changing "OP2" to "o2p", part of my problem have been solved. but the
> problem I haven't shown you still exist:
> "FATAL: Atom .R<DA 1>.A<HO5' 33> does not have a type.
> FATAL: Atom .R<DA 1>.A<H5' 34> does not have a type.
> FATAL: Atom .R<DA 1>.A<H5'' 35> does not have a type.
> FATAL: Atom .R<DA 1>.A<H2' 36> does not have a type.
> [snip]
>
> FATAL: Atom .R<DT 50>.A<HO3' 37> does not have a type"
> could you please tell me the "old" code for these"H2'34"thing? thank you
> very much and wish you have a good day!
>
Do you have a reason not to update to AmberTools 14 and use a modern force
field? If you do, your PDB file will work without having to modify it, AND
you will get better force fields. It will be difficult to get a simulation
using old force fields accepted in peer-reviewed journals when demonstrably
superior alternatives exist.
That said, the atom names in the template are in the
$AMBERHOME/dat/leap/lib library files (probably something like
all_nucleic94.lib, or something). Again, use of these old force fields is
strongly discouraged (unless you are doing some type of comparative study
to show their deficiencies) -- you would be much better off downloading the
latest version of AmberTools and using the latest force fields there
instead.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 04 2015 - 08:30:02 PST
