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problem with residue detection

alfredoq
Dear all:

I am having some problem with the conversion of a .smi file to a .mol2
structure. The .smi notation is:

OC[C@@H]1CCCN1C(=O)[C@H](Cc1c[nH]c2ccccc12)Nc1ccc(Nc2ccncc2)cc1


after applying the following script:

obabel -ismi file.smi -omol2 -O file.mol2


I obtain a .mol2 file in which residues are named TRP and UNK, and it
seems like the molecule es detected as containing 2 residues. Is obable
recognizing a tryptophan residue in my organic molecule and it is
assignig it as a residue?
How can I skip this detection?

thank you very much in advance for the help,

best regards

Alfredo

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Re: problem with residue detection

mwojcikowski
Hi,

Add "-xl" to the command line (which ignores the residues for mol2).

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
[hidden email]

2016-04-11 19:08 GMT+02:00 Fredy Quevedo <[hidden email]>:
Dear all:

I am having some problem with the conversion of a .smi file to a .mol2
structure. The .smi notation is:

OC[C@@H]1CCCN1C(=O)[C@H](Cc1c[nH]c2ccccc12)Nc1ccc(Nc2ccncc2)cc1


after applying the following script:

obabel -ismi file.smi -omol2 -O file.mol2


I obtain a .mol2 file in which residues are named TRP and UNK, and it
seems like the molecule es detected as containing 2 residues. Is obable
recognizing a tryptophan residue in my organic molecule and it is
assignig it as a residue?
How can I skip this detection?

thank you very much in advance for the help,

best regards

Alfredo

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gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532
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reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532
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