Re: [AMBER] For format correction after generating solvent file.

From: David A Case <>
Date: Fri, 6 Sep 2013 11:17:14 -0400

On Fri, Sep 06, 2013, Krati Sharma wrote:

> a. This is what in my actual file
> ATOM 11531 CB GLNB 717 47.313 -3.313
> -15.627

Above looks correct, assuming that the "A" in ATOM is in column 1.

> On running tleap, it shows error (try.png)
> FATAL: Atom .R<GL 717>.A<CB 3> does not have a type.

Can you send a small pdb file that shows the problem? Make sure that the
residue name is in columns 18-20. (If it is not, there is no need to send
the file, just fix it. But the snippet you show above appears to have the
residue in the proper columns.)

> b. When I reduce the gap between ATOM and 11532 (see below) I get
> .top and .crd file
> ATOM 11532 CG GLNB 717 47.822 -1.912 -15.233 (actual file-
> Result in error)

Of course: the entries here are in the wrong columns. But it is not clear from
your description exactly how you arrived at this file. If there is a bug,
we would need to be able to reproduce it here. So you need to create a small
example with all the information someone else would need to get the same

(A note: your earlier email implied that you were using the output
from ambpdb. But that program always puts spaces after the residue name,
so it is unlikely that it would output a file with something like "GLNB" in
it. Please double-check that you are not mixing up filename somehow.)


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Received on Fri Sep 06 2013 - 08:30:02 PDT
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