Re:

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Feb 19 2020 - 01:36:55 CST

Hi Josh
You are right and I apologize for having posted my question about a (silly)
wrongly built system: in this larger version of the sphere cutting the
RNA-protein-ligand system, before running AutoPSF, I forgot to adapt the
X-ray-defined atom names of the ligand to the atom names in the ligand
parameter file. Moreover, I took for granted the obtained psf/pdb without
examining the .log file, which contains clear warnings, and/or the VMD
graphics, which showed a highly distorted ligand.

Sorry
francesco pietra

On Tue, Feb 18, 2020 at 10:37 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:

> Minimization was not successful. You've got a long bond somewhere or bad
> geometry that splits your geometry past adjacent patches, or at least that
> is why I get global count errors. You'll see warnings in the log to this
> effect.
> -Josh
>
> On Tue, Feb 18, 2020, 1:34 PM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> Hello
>> With a large system (RNA-protein in TIP3, Atoms: 1352778) after
>> successful minimization, first by restraining RNA and the protein, while
>> minimizing TIP3 MG ZN2 SOD, then without any restraint, at heating, with
>> either ts=0.5fs or 0.1fs the error arises
>>
>> TCL: Running for 500000 steps
>> REASSIGNING VELOCITIES AT STEP 0 TO 1 KELVIN.
>> FATAL ERROR: Bad global bond count! (984320 vs 984325)
>>
>> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>>
>> There is some precedent for such curious error, however unresolved
>> *From:* Peterson J (*peterson.jjjj_at_gmail.com*
>> <peterson.jjjj_at_gmail.com?Subject=Re:%20FATAL%20ERROR:%20Bad%20global%20bond%20count!>
>> )
>> *Date:* Wed Jun 12 2013 - 11:01:23 CDT
>>
>> thanks for advice
>> francesco pietra
>>
>>

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