Re: [AMBER] dlpc membrane

From: David A Case <>
Date: Mon, 14 Nov 2016 21:00:17 -0500

On Mon, Nov 14, 2016, wrote:

> here I send you the pdb file and the tleap file.

OK: here's the problem: the leaprc.water.tip3p file has a residue called "LA",
which overwrites the lipid14 residue of the same name. [In my partial
defense, if you had followed the suggestions in my earlier email, this would
have become obvious.]

This is a general problem we have: Amber developers often feel free to invent
their own residue names, that may conflict with those defined by the PDB.
In this case, "LA" is a PDB-reserved name for the La(III) ion, and is
correctly used in leaprc.water.tip3p. The leaprc.lipid14 file is trying to
re-use this name for something entirely different.

A workaround for this case should be (untested!) to load leaprc.water.tip3p
first, then leaprc.lipid14 second.

Thanks for the report--we'll have to try to figure out a better long-term


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Received on Mon Nov 14 2016 - 18:30:02 PST
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