Dear Prof. Case,
Thanks for your good suggestions. I tried to run without -tip3_flex flag. But the same error message is there.
Best wishes
Duan Baogen
From: David A Case
Date: 2013-04-12 19:49
To: dbaogen; AMBER Mailing List
Subject: 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
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 Sat Apr 13 2013 - 23:30:02 PDT
