[AMBER] loading a mol2 file in xleap

From: <vallespardojl.chem.leidenuniv.nl>
Date: Fri, 24 Jul 2009 18:40:13 +0100

Dear AMBER users,

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 Fri Jul 24 2009 - 18:07:12 PDT
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