AMBER Archive (2003)

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

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Wed May 21 2003 - 12:12:17 CDT

Actually I did MD simulation for my organic molecule with water. I try
to use MM_PBSA to decompose the energy from the MD trajectory file. Last
time when I did the same thing for another molecule.I got same kind of
error, like 'bad atom type c', then I got a bug fix file from the amber
web page and recompiled the program. Then It works. But unfortunately
there is no fluorine in that file. I don't know how I can get parameters
for fluorine to modify that bug fix file.

Lishan

On Wed, 2003-05-21 at 11:17, David A. Case wrote:
> On Wed, May 21, 2003, Lishan Yao wrote:
>
> > 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?
> >
>
> It's still very hard to know, give so little information about what you did.
>
> It looks like you are probably trying to use the sander "LCPO" approximation
> to get surface areas, but (as implemented) this routine doesn't know how
> big fluorine atoms are. You may need to modify mdread.f to make fluorine
> look like carbon, say.
>
> ..good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>