Re: [AMBER] Problem on making inpcrd file

From: David A Case <>
Date: Sun, 27 Jul 2014 23:52:27 -0400

On Sun, Jul 27, 2014, 肖立 wrote:

> I use the amber14 tleap to generate an inpcrd file. I shows the
> following message:
> "
> Checking Unit.
> WARNING: There is a bond of 0.284304 angstroms between:
> ------- .R<NAP 262>.A<C1B 12> and .R<NAP 262>.A<N9A 13>
> WARNING: There is a bond of 0.255071 angstroms between:
> ------- .R<NAP 520>.A<C1B 12> and .R<NAP 520>.A<N9A 13>

You should certainly look into what is causing these problems; other things
may also be wrong.

> The inpcrd file is not generated right. It misses several coordinate
> information as well as the box information.

We would need more information. The lack of box information suggests that
maybe you didn't set the box in tleap: did you use setBox, or solvateBox,
solvateOct? Those are the most common commands that set the box info.

Missing coordinates might arise from having duplicate atom names within a
residue. But since we don't know what commands you gave to tleap, and don't
have any details of what is "wrong" with the inpcrd file, it's hard to give
much good advice.


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Received on Sun Jul 27 2014 - 21:00:02 PDT
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