Re: AMBER: antechamber --> sander problem

From: David A. Case <>
Date: Fri, 16 Nov 2007 13:17:50 -0800

On Fri, Nov 16, 2007, Yamada, Takahiro wrote:
> I have a special system which is butadiene-acrylonitrile-butadiene
> monomer solvated with TIP3PBOX. I exactly followed Tutorial B4 (sustiva
> solvated with TIP3PBOX) to make prmtop and inpcrd. Then I tried to run
> sander, but I failed to run. The end on output file said "Error:
> ifbox=2 in prmtop but angles are not correct." Attached are prmtop,
> inpcrd, out, and 2 pdb files (one for original
> butadiene-acrylonitrile-butadiene monomer, and one for monomer solvated
> with water which I recreated using ambpdb command). I appreciate if
> anyone could tell me what is wrong. I am new AMBER user and trying to
> apply AMBER code to model polymer - organic solvent interaction. I
> created this system as a 1st step to examine if AMBER can be used for my
> research.

In your input file, you set ntb=0, but this would not be correct for a
solvated system, which is always periodic.

Sander gets confused at this point. It should give a better error message
(e.g. check first that ntb=0 but a nonzero ifbox). Still, the fix should be
easy: don't set ntb=0 for periodic simulations.

...good luck...dac

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Received on Sun Nov 18 2007 - 06:07:52 PST
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