Hello,
FYI I've never used MAWS. I hope someone familier to this program will
be able to answer you...
Anyway, from your message:
- Question 1& 2: you don't see the nucleotide residues using the `list`
command in tleap because I guess that you loaded only
leaprc.protein.ff19SB. tleap default load commands have changed since a
couple of years. Now you need to load specifically the force field(s)
you want. The output example from Tutorial 4B is outdated. If you do
'source leaprc.DNA.bsc1', then 'list' in tleap, you will see the
residues you're looking for appear.
- Question 3: I can't answer directly since I'm not a MAWS user. But my
2 cents are that since the github source from MAWS is more than 4 years
old, you are not loading the correct libraries/force fields. Try to dig
into the source code and add the correct leaprc/etc to include DNA
definitions (and others like protein, water, etc.). With a little bit of
luck, that should make it.
Best,
Gerald.
On 8/25/19 22:06, Bruno Cramer wrote:
> 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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>
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Received on Mon Aug 26 2019 - 07:00:02 PDT
