AMBER Archive (2006)

Subject: RE: AMBER: Where to modify the atom type in sander?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jan 05 2006 - 10:12:34 CST

Hi Zhli,

Try this:
http://www.google.com/search?sourceid=navclient&ie=UTF-8&rls=GGLG,GGLG:2005-
52,GGLG:en&q=bad+atom+type+F

and this

http://amber.ch.ic.ac.uk/archive/200305/0162.html

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of zhli_2000_at_126.com
> Sent: Thursday, January 05, 2006 01:21
> To: amber_at_scripps.edu
> Subject: AMBER: Where to modify the atom type in sander?
>
>
>
> Dear all,
>
> When I use mm_pbsa to calculate DC, the error is the following:
> ---------------
> $ bad atom type: F
> /data/amber8/exe/sander -O -i sander_com.in -o
> sander_com.1.out -c
> ./min_cyc16_com.crd.1 -p ./mincomplex.top not successful
>
> ---------------
> There exits F atom in my ligand file. The above question
> seems that sander
> is something wrong.
>
> How to modify this? Please give me some advices.
>
> Thank you in advance!
>
>
>
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