Dear Users,
I was trying to simulate a single strand TT( thymine-thymine) with amber 10
or amber 11. The sample was created using make-na server (single strand)
or 3DNA (double strand, I use chimera to extract the single strand). Having
the single strand DNA, I was not able to obtain the prmtop file via xleap.
I would like to know if there is a way to generate the prmtop file. Since I
have performed the simulation in gromacs with unified amber force-field. in
gromacs, I have changed T to DT..
Furthermore, according to Ross tutorial the DNA constructed with NAB should
work without problem, regarding make-na server, it is based on NAB.
I would really want to use the feature of some QM in amber11.
Please let me know if there is a way to generate this prmtop file.
Best regards
Collins
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Received on Tue Aug 13 2013 - 09:30:02 PDT
