Re: [AMBER] A problem in using tLeap

From: David A Case <>
Date: Mon, 15 Jun 2015 17:19:38 -0600

On Mon, Jun 15, 2015, Morteza Chehel Amirani wrote:
> I have a mol2 input file in which 2 non-bonded residues exists. I used
> tLeap to add ions and solvate the residues, and then saved the new file in
> mol2 format. The problem is that the two residues become one residue in the
> new file, which makes the simulation fail in Amber.

The mol2 support in tleap does not cover all possible uses; basically, the
main use of mol2 files is for single molecules.

1. When you add ions and solvate the residues, you should use saveAmberParm
to create Amber files for a future simulation, or savePdb to save the
coordinates. You can create a mol2 file with saveMol2, but it might be
garbled, and could not be used for future calculations in Amber.

2. If using saveAmberParm rather than saveMol2 doesn't help, split your
original mol2 file into two files, one for each molecule. Then load both
into tleap.

...good luck....dac

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Received on Mon Jun 15 2015 - 16:30:03 PDT
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