Hi,
If I remember correctly, this might be caused by your atom arrangement in
your structure file. You didn't specify which version of sander you used, but
in sander6, GB used to require that hydrogen atoms follow their bonding heavy
atoms. Otherwise, it will complain and stop. (atom 19 should be a hydrogen
atom if this's the reason). I hope this helps.
On Monday 05 May 2003 07:57, tang kwa wrote:
> Dear all,
>
> I have a question about the minimization. I would like
> to check the frcmod file. So I will compare the
> minimized structure from AMBER with Gaussian. However
> I could not minimize the molecule. This is my input
> file:
>
> &cntrl
> imin = 1, maxcyc = 500, ntpr = 25,
> igb = 1, ntb = 0, cut = 10.0,
> &end
>
> the out showed that
> NATOM = 64 NRES = 1
>
> MAXCYC= 500 NCYC = 10 NTMIN = 1 DX0
> = 0.010000
> DXM = 0.50000 DRMS = 0.00010
>
> Water definition for fast triangulated model:
> Resname = WAT ; Oxygen_name = O ; Hyd1_name =
> H1 ; Hyd2_name = H2
> Using modified Bondi radii and Tinker screening
> parameters
> Unable to find bonded partner for atom 19
>
>
> I will appreciate it if anybody can figure out this
> problem.
> One more question, is it possible to minimize without
> IGB(IGB=0)?
>
> Thank you in advance,
> TK
>
>
> __________________________________
> Do you Yahoo!?
> The New Yahoo! Search - Faster. Easier. Bingo.
> http://search.yahoo.com
--
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790
Received on Mon May 05 2003 - 14:53:02 PDT
