Re: [AMBER] Prep file is empty

From: David A Case <>
Date: Thu, 30 Jan 2014 07:59:08 -0500

On Thu, Jan 30, 2014, DEBOSTUTI GHOSHDASTIDAR wrote:
> We need the prep file because we will be generating an frc file with
> parameters taken from literature and not the ones in Amber library.

I guess I don't understand this comment; we're trying to remove anything that
requires a prep format file. But if you do need it, can you just edit the
prep file and put the correct values in place of the "nan"s?

Note: if you just want to get on with things, all files you need for BF4- are
given in tutorial A15. And you can hand-edit those if you want different
parameters ("from the literature").

If you really want help in figuring out why antechamber is giving an odd prep
file (even thought the mol2 file is fine), you'll have to send all the files
you are using so that someone else can reproduce what is happening.


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Received on Thu Jan 30 2014 - 05:00:02 PST
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