[gmx-users] Help: No default LJ-14...

[David van der Spoel]

On Thu, 2003-11-20 at 09:00, Henrik Rundgren wrote:
> hello all.
> I have a problem.
> I have run some simulations with Gromacs, and all seems fine.
> No I try to run a small peptide in wter, and I get the following warnings:
> 
>  Generated 1179 of the 1378 non-bonded parameter combinations
> WARNING 1 [file "top.top", line 86]:
>   No default LJ-14 types, using zeroes
> WARNING 2 [file "top.top", line 87]:
>   No default LJ-14 types, using zeroes
> WARNING 3 [file "top.top", line 88]:
>   No default LJ-14 types, using zeroes
> WARNING 4 [file "top.top", line 109]:
>   No default LJ-14 types, using zeroes
> WARNING 5 [file "top.top", line 110]:
>   No default LJ-14 types, using zeroes
> WARNING 6 [file "top.top", line 111]:
>   No default LJ-14 types, using zeroes
> Excluding 3 bonded neighbours for Protein 1
> Excluding 2 bonded neighbours for SOL 884
> 
> Then it continues and makes the infile .trp, but I doubt that this is ok 
> to run an simulation on....
> I have checked in the topology file, and the default type value is 1 
> (=LJ)... so I don't see where this warning is coming from.
> 

have you checked which atom pair is listed in top.top lines 86, 87, 88,
109-111

> thanks for the help.
> sincerely,
> henrik
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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