Re: [AMBER] How to use set pert=true

From: David A Case <>
Date: Wed, 20 May 2020 13:43:27 -0400

On Wed, May 20, 2020, Dawid das wrote:
>When I use tleap to generate my parm file, I get an error
>Bond: maximum coordination exceeded on A<N 7>
> -- setting atoms pert=true overrides default limits

How many atoms are bonded to this particular nitrogen? Are you sure
that this odd coordination is what you expect?
>I have tried many times to use set like this:

>set x.66.N pert=true
>set default x.66.N pert=true

I don't think tleap would ever use an "=" construct like this.
You should try this:

set x.66.N pert true

(I'm just going by the output of "help set" inside tleap.)

But I'm concerned that (even if it works) it may just be hiding
something deeper that is wrong with your input.


AMBER mailing list
Received on Wed May 20 2020 - 11:00:02 PDT
Custom Search