Dear AmberUsers!
I would like to use periodic boundary-conditions of DNA (infinite long
DNA), therefore the molecule has bounds beyond the boundary.
I used "nab" to create the Molecule (similar to Amber-Tutorial B1
<
http://ambermd.org/tutorials/basic/tutorial1/>), which worked out fine.
Due to the reason that it should be infinity long, I removed the
end-sequences (*nuc10.pdb*), then I got problems:
I loaded the molecule into LEAP (*LeapVorbereitung.leap*) using
> nuc10= loadpdb "nuc10.pdb"
then I get following messages (*tleapDNA.log*):
> Loading PDB file: ./nuc10.pdb
> Created a new atom named: P within residue: .R<DA5 1>
> Created a new atom named: OP1 within residue: .R<DA5 1>
> Created a new atom named: OP2 within residue: .R<DA5 1>
> Created a new atom named: P within residue: .R<DT5 11>
> Created a new atom named: OP1 within residue: .R<DT5 11>
> Created a new atom named: OP2 within residue: .R<DT5 11>
> total atoms in file: 640
> Leap added 4 missing atoms according to residue templates:
> 4 H / lone pairs
> The file contained 6 atoms not in residue templates
Those atoms shouldn't be added, because they are on the other side of
the boundary. I even tried it with different cutting points, but it
never worked out.
When I want to save the file using:
> saveamberparm nuc10 nuc10.prmtop nuc10.inpcrd
I get following error-Messages:
> Checking Unit.
> FATAL: Atom .R<DA5 1>.A<P 31> does not have a type.
> FATAL: Atom .R<DA5 1>.A<OP1 32> does not have a type.
> FATAL: Atom .R<DA5 1>.A<OP2 33> does not have a type.
> FATAL: Atom .R<DT5 11>.A<P 31> does not have a type.
> FATAL: Atom .R<DT5 11>.A<OP1 32> does not have a type.
> FATAL: Atom .R<DT5 11>.A<OP2 33> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
I'll be searching a wile, but wasn't able to find anything helpful, also
someone else had the same Error-Message before:
http://archive.ambermd.org/201212/0120.html
But it was due to the fact hat he had used different names for the
variable name in leap and another name of the .pdb-File
http://archive.ambermd.org/201212/0122.html
I use the same name, but changing the names to different ones also
didn't help.
The protein database (*nuc10.pdb*) the Leap-Inputfile
(*LeapVorbereitung.leap*) and the Leapoutput (*tleapDNA.log*) are attached.
To be able to continue my research, I will first have to solve this issue.
Any help/comment would be highly appreciated.
Best Regards
Johannes Kalliauer
PhD-Student at TU Wien
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Received on Wed Jun 21 2017 - 07:00:04 PDT
