AMBER Archive (2007)

Subject: Re: AMBER: bad atom type errors in GB for halides?

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Apr 12 2007 - 14:57:13 CDT

Dear David,

I have seen this error message in one of my simulations when I tried to
use gbsa (which is to include the Solvent Accesible Surface Area - SASA -
in the calculations). I think you need to define those missing gbsa
parameters for the atom types that are used in your system. You need to
modify the $AMBERHOME/src/sander/mdread.f file (if I am wrong here, please
someone correct me). For instance, go to the line 1054 in
$AMBERHOME/src/sander/mdread.f check out the code written below that line.
Good luck.

Best,

On Thu, 12 Apr 2007, David Mobley wrote:

> All,
>
> This is probably naive, but I'm trying to run some simulations of
> various small molecules in GB solvent. This includes some things like
> bromomethane, etc. I can set them up fine with tleap (no
> warnings/errors), but when I go to run in GB solvent, I get an error
> like "bad atom type: br". Vacuum works fine, so I assume this is an
> issue with GB parameters for these? This is with igb=5. Would I need
> to derive my own parameters for these, or are there other options?
> What would I need to edit and provide in order for this to work OK?
>
> Thanks,
> David
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
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