From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jan 05 2015 - 03:19:13 CST
That’s weird, I think one of your input files is corrupted or of wrong format. Maybe an additional pdb for constraints or fixed atom etc or a restart file?
Von: amin_at_imtech.res.in [mailto:amin_at_imtech.res.in]
Gesendet: Montag, 5. Januar 2015 09:51
An: Norman Geist
Betreff: Re: AW: namd-l: warnings while using amber files
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 PRESSURE
Info: LONG-RANGE LJ: AVERAGE A AND B COEFFICIENTS -1.42444e+06 AND -1325.18
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.
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:
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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