Date: Mon Jan 05 2015 - 02:50:52 CST
Thanks. It's a relief that these warnings are harmless. The lines
containing error have just "ERROR" written, nothing else e.g.
Info: LONG-RANGE LJ: APPLYING ANALYTICAL CORRECTIONS TO ENERGY AND
Info: LONG-RANGE LJ: AVERAGE A AND B COEFFICIENTS -1.42444e+06 AND
There are hundreds of such lines. After these lines the simulation runs
and I can't see anything obviously wrong with the results.
On 2015-01-05 12:12, Norman Geist wrote:
> I think we should see the ERROR lines, too, as the lines you have posted are not an error. NAMD just tells that it skipped unused sections of the parmtop.
> Norman Geist.
> VON: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] IM AUFTRAG VON amin_at_imtech.res.in
> GESENDET: Freitag, 26. Dezember 2014 04:55
> AN: Namd l
> BETREFF: Re: namd-l: warnings while using amber files
> I think I should add that I am using NAMD-2.9 x64 (ibverbs) and ambertools 14.
> On 2014-12-25 16:44, amin_at_imtech.res.in wrote:
>> Dear all,
>> I am trying to run a simulation with amber prmtop and inpcrd files made using tleap. I have used amber ff14sb force field. In the log file I get the following warnings:
>> PARM file in AMBER 7 format
>> Warning: Skipping ATOMIC_NUMBER in parm file while seeking MASS.
>> Warning: Skipping SCEE_SCALE_FACTOR in parm file while seeking SOLTY.
>> Warning: Skipping SCNB_SCALE_FACTOR in parm file while seeking SOLTY.
>> Warning: Encounter 10-12 H-bond term
>> Warning: CORRECTION OF ZERO MASS ATOMS TURNED OFF BECAUSE LONE PAIRS ARE USED
>> Warning: Found 32738 H-H bonds.
>> Then I get many lines where only "ERROR" is written.
>> Can someone please help me with this?
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