David,
I have been using leaprc.ff10. When I convert the pdb file generated in nab to an amber pdb with ambpdb I obtain a file that looks like this:
ATOM 1 HO5' G5 1 3.429 -7.861 3.641 1.00 0.00
ATOM 2 O5' G5 1 4.232 -7.360 3.480 1.00 0.00
ATOM 3 C5' G5 1 5.480 -8.064 3.350 1.00 0.00
ATOM 4 H5' G5 1 5.429 -8.766 2.518 1.00 0.00
ATOM 5 H5'' G5 1 5.679 -8.609 4.273 1.00 0.00
I have been told that the reside names are not in a correct AMBER format. Is this true or am I doing something incorrect here?
thanks,
Charlie
On Aug 11, 2011, at 4:44 PM, case wrote:
> On Thu, Aug 11, 2011, Charles Johnson wrote:
>
>> I am currently working through the AMBER tutorials for NMR refinement
>> of a DNA duplex. However, I am using RNA and came across this
>> statement: If you were working with RNA instead of DNA, you would want
>> to source $AMBERHOME/dat/leap/cmd/leaprc.rna instead of the default
>> $AMBERHOME/dat/leap/cmd/leaprc (which assumes the nucleic acid residues
>> are DNA). I am not sure how or where to implement this change. Any
>> help would be appreciated.
>
> The tutorial is out of date. Before the introduction of PDB format 3, the PDB
> standard for residue names was the same for DNA and RNA(!), and special
> features were needed to tell Amber programs which was which.
>
> This is no longer necessary, if you use an up-to-date leaprc like leaprc.ff10.
> Thanks for the reminder that we need to update the tutorial. But as always,
> treat tutorials as guides, recognizing that sometimes you need to follow the
> spirit, not the letter. Also, be sure you can run (short) unconstrained
> simulations of whichever nucleic acid you want, before jumping into restrained
> problems.
>
> ....dac
>
>
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Received on Fri Aug 12 2011 - 06:30:03 PDT
