On Wed, Oct 04, 2023, Fadaei Fatemeh Mgr. via AMBER wrote:
>
>thank you so much for your information. I did the following commands in
>tleap but I still get the same error? should I do somethings else?tleap
>Source: /my/path/leaprc.ff99
The path to leaprc.ff99 is in the "oldff" folder for a reason: no one should
be using this quarter-century-old parameterization any more. I'm not even
sure that the atom and residue nomenclature are up to modern standards.
>loadoff terminal_monophosphate.lib
After you do this: use the "list" and "desc" commands in tleap to examine
what has been loaded. Make sure that whatever residue name you are using
for your 5' nucleotide has a phosphate group in the tleap unit that is being
accessed.
>dna = loadpdb my_file.pdb
Look carefully at the errors that come here. You will need to learn how to
examine tleap units (say by using the "desc" command), and will need to
manually compare the pdb residue and atom names to those in the DA5 unit you
have loaded.
>>"Atom P in residue DA1 was not found in rtp entry DA5 with 30 atoms while sorting atoms."
Can you say (again?) exactly how you got this error? What program were you
running?
...thx...dac
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Received on Wed Oct 04 2023 - 07:30:02 PDT
