Re: [AMBER] loading a mol2 file in xleap

From: FyD <>
Date: Mon, 27 Jul 2009 14:44:50 +0100

Dear Jose Luis,

> Thanks for the help, but I check my file with the model that you send
> me and I think that the structure is the same. In this mail I attached
> my mol2 file if you want compare.

No, you do not have the .<TRIPOS>SUBSTRUCTURE Section as in

Moreover, what are these "Du" atom name ?
Are you sure Antechamber recognizes these "Du" atom name ? I do not think so.

Finally, this structure is quite big & repetitive fragments could be
designed. My feeling is that you should split this molecule into more
elementary units/residues.

regards, Francois

> Quoting FyD <>:
>> Dear Jose Luis,
>> Are you sure the Tripos moL2 file format generated is correct ?
>> See
>> See for instance
>> If your molecule is too big, you could split it in more elementary elements.
>> regards, Francois
>>> I want run a molecular dynamics job with AMBER8, and I have my molecule
>>> in a mol2 file generated with the Spartan.
>>> For start the molecular dynamics with the sander I need first a
>>> coordinate and topology file, and for this purpose I use the xleap.
>>> For load the mol2 file I use this command:
>>> LIG=loadmol2 name_of_my_file.mol2
>>> and I don't obtain any error, but when I use the command "list" the LIG
>>> residue doesn't appear in the list.
>>> Why happens this? How can I solve it?
>>> regards,
>>> Josť Luis
>>> P.D.: I know the possibility of generate a prepin file with the
>>> antechamber, but my molecule is too big for this sub program.

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Received on Mon Jul 27 2009 - 10:09:38 PDT
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