AMBER Archive (2009)

Subject: Re: [AMBER] loading a mol2 file in xleap

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jul 24 2009 - 15:00:41 CDT

Dear Jose Luis,

Are you sure the Tripos moL2 file format generated is correct ?
See http://tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0

See for instance
http://q4md-forcefieldtools.org/REDDB/projects/W-1/tripos1.mol2

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,
>
> José 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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