Re: [AMBER] Generation of parameter files of transmembrane protein system via xleap

From: David A Case <>
Date: Mon, 14 Nov 2016 07:47:21 -0500

On Mon, Nov 14, 2016, Mahrukh Imtiaz wrote:

> I am trying to generate parameter files for transmembrane protein system
> via xleap but I am facing some issues. When I give the command of
> saveamberparm to generate prmtop and inpcrd fis, it generates the files
> but the structure of lipid gets a little distorted. It would be a great
> help if anyone could guide me where am I making mistake.

I think you will have to explore some more, in order to provide more
information. When you say "the structure of lipid gets a little distorted",
what exactly do you mean? How did you draw this conclusion? LEaP just
transfers the atomic coordinates from the input to the output (trying to
generate coordinates for missing atoms if needed.) So, the xyz coordinates in
your inpcrd file (created by LEaP) should be the same as in your input file.
If that is not the case, we need more information about what you did.

If the structure is only a "little" distorted, perhaps that can be fixed by
minimization or's really impossible to know.


AMBER mailing list
Received on Mon Nov 14 2016 - 05:00:03 PST
Custom Search