On Tue, Jan 08, 2013, Chandrasekaran, Suryanarayanan wrote:
>
> I was trying to make comparison between FF Charm and AMber so i built a
> TIP4P box in charmm and gave the PDB file as input to leap and made it
> recognize the atoms and while writing the .prmtop and .inpcrd file i am
> getting warning
>
> 1-4: angle 9854 9855 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> what is the problem?
This is not an error message, but is not usually seen (unless you are running
an old version of AmberTools.) Without knowing what commands you gave
to LEaP, one cannot be sure that you have done everything correctly.
You need commands like "WAT=T4E", "loadAmberParams frcmod.tip4pew", and
"set <unit> box { x y z }".
> When i run the simulation in namd I got a warning:
>
> Warning: Encounter 10-12 H-bond term
> Warning: CORRECTION OF ZERO MASS ATOMS TURNED OFF BECAUSE LONE PAIRS ARE USED
> Warning: Found 2429 H-H bonds.
> ERROR
This is a namd problem that I can't give any advice on. But it would
certainly be advisable to run a short simulation in Amber itself, if you want
to check that the Amber results are giving you what you want.
....dac
p.s.: If you want to see what Amber prmtop and inpcrd files look like for a
box of TIP4P water, look at the files in $AMBERHOME/test/tip4p.
p.p.s: I'd strongly recommend using TIP4P-ew for any real simulations, rather
than the original TIP4P, at least if you are running the simulations in Amber
using PME.
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Received on Wed Jan 09 2013 - 06:30:05 PST
