AMBER Archive (2008)

Subject: AMBER: Re: bad atom type f(fluorine) in MM-PBSA

From: kanazta1_at_yahoo.co.jp
Date: Mon Feb 04 2008 - 11:32:51 CST

Dear all,
   
  Does anybody know if there has been any update regarding the LCPO paramaterization of fluorine ?
   
  regards,
  Takanori
   
  ------------------------------------------------------------------
  Subject: Re: bad atom type f(fluorine) in MM-PBSA?From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Wed May 21 2003 - 10:49:20 CDT
   
  Lishan Yao wrote:
>
> Hi:
> There is one fluorine atom in my organic molecule. I use MM-PBSA to do
> some calculation. But I get an error message: bad atom type f. What
> should I do?
  The error occurs because F has not been parameterized for the LCPO model
(s. Weiser et al., JCC 1999, 20,217), which is used to calculate the
solvent-accessible surface area for GBSA calculations within sander. If
you "come up" with some reasonable parameters for this, you can add
these parameters to the list in mdread.f (in $AMBERHOME/src/sander; see
the code after
"c --- construct parameters for SA calculation; note that the
 c radii stored in L165 are augmented by 1.4 Ang.
"
).
  Alternatively (and probably the easier way), you might want to determine
the SAS by using molsurf (set MS=1 in the mm_pbsa.in file). Have a look
at the "atmtypenumbers" file, to make sure that the atomic radius for F
is included there.
  Best regards
  Holger
>
> Sincerely
> Lishan
  
-- +++++++++++++++++++++++++++++++++++++++++++++

Dr. Holger Gohlke

Dept. of Molecular Biology, TPC15

The Scripps Research Institute

10550 N. Torrey Pines Rd.

La Jolla CA 92037 USA

phone: +1-858-784-9788

fax: +1-858-784-8896

email: gohlke_at_scripps.edu

+++++++++++++++++++++++++++++++++++++++++++++

 

 
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