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
loadoff terminal_monophosphate.lib
dna = loadpdb my_file.pdb
savepdb dna P5_my_file.pdb
quit
On Monday, October 02, 2023 15:44 CEST, David A Case <david.case.rutgers.edu> wrote:
On Sat, Sep 30, 2023, Fadaei Fatemeh Mgr. via AMBER wrote:
>
>"Atom P in residue DA1 was not found in rtp entry DA5 with 30 atoms while sorting atoms."
The default in Amber is that 5' nucleotides do not have a phosphate group
(since this is quite common with synthetic samples). If you want a
phosphate group, load terminal_monophosphate.lib after you load the regular
RNA or DNA libraries -- this will change the defaults.
...hope this helps....dac
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Received on Wed Oct 04 2023 - 06:00:02 PDT
