Dear Dr. Case,
Thank you very much for your help! The prmtop file was generated, and minimization ncyc could run as long as it was set to run, such as 50000, but minimization with conjugate gradient failed after several thousands of steps. Is this an indication that the structure had problems if the first step of minimization with steepest descent results in VDWAALS = ************* even for a huge system?
Thanks!
Wen
________________________________
From: David Case <david.case.rutgers.edu>
Sent: Thursday, July 13, 2017 12:01:10 PM
To: AMBER Mailing List
Subject: Re: [AMBER] ERROR: The unperturbed charge of the unit: is not integral
On Thu, Jul 13, 2017, Li, Wen wrote:
>
> After a pdb was loaded to leap in order to set up a pmemd run for an
> RNA+protein system, saveamberparm failed due to the unperturbed charge
> of the unit is not integral, for example, the charge may be -14.5 or
> 30.6 etc. Could you please tell me how to get rid of the problem.
This message is only an informational message. If your LEaP failed to produce
a prmtop file, there must have been some other problem. Please look at the
outputs (and the leap.log file) carefully to look for errors.
.....dac
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Received on Fri Jul 14 2017 - 07:00:02 PDT
