Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program

From: David A Case <case.biomaps.rutgers.edu>
Date: Fri, 12 Apr 2013 07:49:01 -0400

On Fri, Apr 12, 2013, dbaogen wrote:
>
> Error: A residue defined as a "fast 3-point water"
> is not defined by a triangle of three bonds.
> Residue 920 contains 2 bonds.
>
> chamber -top top_all27_prot_lipid_na.inp -param
> par_all27_prot_na.inp -psf ${str}_charmm.psf -cmap -tip3_flex
> -crd ${str}.pdb -p ${str}.prmtop -inpcrd ${str}.inpcrd
> -verbose

Try running without the -tip3_flex flag. You are asking for a flexible water
model, but other parts of the workflow are expecting the (standard) rigid
tip3p model.

(Caveat: I'm no expert on chamber, but this looks like it is worth a try.)

...dac


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Received on Fri Apr 12 2013 - 05:00:03 PDT
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