AMBER Archive (2003)

Subject: Re: AMBER: question about input files for small molecule with fluorine

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Nov 03 2003 - 09:53:49 CST

this error is because you chose to calculate surface
area and sander doesn't have surface area parameters
for F (at least in version 7). It doesn't have to do with
force field atom types, just surface area parameters.
Try without surface area to make sure that this is the
problem (use gbsa=0).
Carlos

----- Original Message -----
From: <aini_at_rwja.umdnj.edu>
To: <amber_at_scripps.edu>
Sent: Monday, November 03, 2003 10:45 AM
Subject: AMBER: question about input files for small molecule with fluorine

> Dear Ambers,
>
>
> I met a wierd probelm with my small molecule with fluorine atom
inside.
> I used antechamber and parmchk to prepare .prep and .frcmod file for it.
> The input file for protein-ligand complex were generated using xleap. when
> I run my minimization with the script "min.in", a error message: bad atom
> type: f and the job was stopped. Why I didn't get complain about atom type
> in xleap?
>
> The content of my min.in:
> cat <<eof > mdin
> minimize structure
> &cntrl
> imin = 1, maxcyc = 1500, ncyc = 1000,
> igb = 2, saltcon = 0.002, gbsa = 1,
> cut = 500,
> ntpr = 50, ntx = 1, ntb = 0,
> ntr = 1,
> &end
> keep all atoms frozen
> 250
> RES 669-919
> END
> END
> eof
> sander -O -i mdin \
> -c AR.crd -p AR.top -ref AR.crd \
> -o AR.min.out -r AR.rst
>
> Thank you very much!
> aini
>
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