Dear Amber user,
I need assistance to try to solve the following problem.
When running the program called MAWS (written in python) it uses
Amber/Antechamber platform for some specific items. It presents the
following output with errors:
-------------------output---------
bcramer.schrodinger:~/workdir-MAWS$ python3 MAWS.py -b 0.01 -i 200 -s 200
-l 15 -t 0.01 -f mol2 PATH INFILE
['DGN', 'DAN', 'DTN', 'DCN']
Choosing from candidates ...
Constructing Ligand/Aptamer complex ...
etc..................
*See complete output in file attached*
----------------------------------
The program MAWS is not finding the files ['DGN', 'DAN', 'DTN', 'DCN']
followed by the prefix *.prmtop and *.inpcrd respectively. It seems to
neglect the files psa38s.prmtop and psa38s.inpcrd.
Looking into Amber literature/Tutorials (based on
http://ambermd.org/tutorials/basic/tutorial4b/) I found a nucleotide table
where 'DGN', 'DAN', 'DTN', 'DCN' are present. For my specific structure and
following the tutorial example, I get for psa38s.mol2 molecular structure,
after typing 'list':
> list
ACE ALA ARG ASH ASN ASP CALA
CARG
CASN CASP CCYS CCYX CGLN CGLU CGLY
CHID
CHIE CHIP CHIS CHYP CILE CLEU CLYS
CMET
CPHE CPRO CSER CTHR CTRP CTYR CVAL
CYM
CYS CYX GLH GLN GLU GLY HID
HIE
HIP HIS HYP ILE LEU LYN LYS
MET
NALA NARG NASN NASP NCYS NCYX NGLN
NGLU
NGLY NHE NHID NHIE NHIP NHIS NILE
NLEU
NLYS NME NMET NPHE NPRO NSER NTHR
NTRP
NTYR NVAL PHE PRO SER SUS THR
TRP
TYR VAL frcmod14SBgaff parm10
------------------
As can be seen 'DGN', 'DAN', 'DTN', 'DCN' are not present.
*QUESTION 1*) Why the nucleotides are not being considered?
*QUESTION 2)* Where can I find the explanation for the 'list' content to
get a better understanding for this output?
*QUESTION 3*) I used psa38s.prmtop and psa38s.inpcrd and produced 'fake
files' DGN', 'DAN', 'DTN', 'DCN' respectively with prefix *.prmtop and
*.inpcrd. This was just to test the MAWS program behavior. MAWS responded
to it but indicates an error: "IndexError: list index out of range"
Can this be understood that the nucleotide library is not present or hidden
somewhere, or ...?
Any help is welcome. Thank you.
Bruno
PS.: One month ago I tried to contact the author of M.A.W.S. but I received
no answer. Details about M.A.W.S. if required can be found (or downloaded)
in
http://2015.igem.org/Team:Heidelberg/software/maws
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Received on Sun Aug 25 2019 - 13:30:01 PDT
