Since you didn't post your complete leap input I can only guess at
what is happening, but the 'desc' command in leap will provide
information about any part of a unit. You just need to make sure
you're specifying the string properly. For example, if I try to
describe the unit DG after loading ff14SB I get:
> desc DG
UNIT name: DG
Head atom: .R<DG 1>.A<P 1>
Tail atom: .R<DG 1>.A<O3' 33>
Contents:
R<DG 1>
The 'Contents:' part tells me that unit 'DG' contains one thing (a
residue) also named 'DG' - that's it. So 'desc DG.1' will properly
describe the residue 'DG' contained within the unit 'DG', but 'desc
DG.2' is invalid since unit 'DG' only contains one residue.
You may find chapters 13.1 and 13.2 on leap in the Amber 15 manual
useful for becoming familiar with leap's concepts of units, residues,
atoms, etc.
Hope this helps,
-Dan
On Thu, Mar 24, 2016 at 10:05 AM, amirhossein taghavi
<amirhosseintaghavi240.yahoo.com> wrote:
> Hello,
> May I ask why 'desc' command in leap can not provide information about different residues of a molecule. I was trying to use 'bond' command in a DNA structure and encountered this.So to say this is the first guanine in the seq:ATOM 29 P DG 2 22.409 31.286 21.483 1.00 0.00
> ATOM 30 OP1 DG 2 23.536 32.157 21.851 1.00 0.00
> .....desc gives information about this one (RESIDUE name: DG
> RESIDUE sequence number: 1
> RESIDUE PDB sequence number: 0.)
>
> but not the next guanine: ATOM 92 P DG 4 24.249 19.412 17.617 1.00 0.00
> ATOM 93 OP1 DG 4 25.420 18.535 17.765 1.00 0.00(desc DG.3
> STRING (with no reference): 'DG.3').
> Thanks in ForwardAmir
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Mar 24 2016 - 09:30:11 PDT
