Thanks a lot.
I was able to obtain the .prmtop and .inpcrd finally.
So, I presume that deleting this line avoids to have a U5 residue as a 5'
terminal and a U3 residue as a 3' terminal, any other atom is accepted as
terminal right?
If that so does this makes sense? For the purpose of simulating RNA, it is
necessary to leave the terminal to achieve better results or even like this
is still acceptable?
Regards
Mahad
2015-01-29 17:24 GMT+01:00 David A Case <case.biomaps.rutgers.edu>:
> On Thu, Jan 29, 2015, Mahad Gatti Iou wrote:
>
> > Loading PDB file: ./chain_B_D.pdb
> > Created a new atom named: P within residue: .R<RU5 13>
> > Created a new atom named: OP1 within residue: .R<RU5 13>
> > Created a new atom named: OP2 within residue: .R<RU5 13>
>
> OK...now you are getting the expected error involving P, which somehow
> didn't
> show up before.
>
> Your RNA has a 5' phosphate group, which is not in the standard Amber
> libraries. The "easy" thing to do is to remove this phosphate if it is
> somehow unimportant for your calculation.
>
> To keep the phosphate, you should make a copy of your leaprc file, find
> the following line:
>
> { 0 "U" "U5" } { 1 "U" "U3" }
>
> and remove it. (This is the line that turns the 5' terminal U into a U5
> residue). Use this modified leaprc file. I've not sure this is all that
> needs to be done, but it should be a good start.
>
> ....dac
>
>
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Received on Fri Jan 30 2015 - 08:00:03 PST
