Hi Qinghua,
Thank you very much for your kind help! It turned out that the structure included a hydrogen atom which is collapsed with another atom. So it seems to work.
Thanks again!
Wen
________________________________
From: Qinghua Liao <scorpio.liao.gmail.com>
Sent: Friday, July 14, 2017 4:50:21 AM
To: amber.ambermd.org
Subject: Re: [AMBER] ERROR: The unperturbed charge of the unit: is not integral
Hello,
I used to have some minimization failure for some system. Then I tried
to do the optimization with MD simulation directly,
at low temperature (i.e. 100K) with small time step (i.e. 1 fs, or 0.5
fs), it worked for me. I once read this suggestion from
the mailing list some time ago. May be you can also give a try with it.
All the best,
Qinghua
On 07/14/2017 03:39 PM, Li, Wen wrote:
> 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 Tue Jul 18 2017 - 08:00:02 PDT
