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?
Norman Geist.
Von: amin_at_imtech.res.in [mailto:amin_at_imtech.res.in]
Gesendet: Montag, 5. Januar 2015 09:51
An: Norman Geist
Cc: namd-l_at_ks.uiuc.edu
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
ERROR
ERROR
ERROR
ERROR
ERROR
ERROR
ERROR
There are hundreds of such lines. After these lines the simulation runs and I can't see anything obviously wrong with the results.
Regards.
Amin.
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.
Amin.
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?
Regards.
Amin.
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