[gmx-users] part2-adding metal-bonding parameters to a force field

[Mark Abraham]

On Apr 5, 2014 7:16 PM, "Ahmet yıldırım" <ahmedo047 at gmail.com> wrote:
>
> Sorry, I get "Message body is too big: 52376 bytes with a limit of 50 KB"
> from list moderator.
>
> I did as you said. I created the ZWA complex in pdb.
> pdb file:
> ...
> ATOM   2080  O   LYS A 261     -24.090 -10.437  34.386  1.00
> 35.64           O1-
> ATOM   2081  ZN  ZWA A 262      -6.760  -2.012  15.320  1.00
> 5.29           ZN
> ATOM   2082  OZ  ZWA A 262      -5.555  -0.748  16.011  1.00
> 8.54           O
> TER    2083      ZWA A 262
> ...
>
> After pdb2gmx command:
> ...
> Linking HIS-94 NE2-754 and ZWA-262 ZN-2081...
> Linking HIS-96 NE2-775 and ZWA-262 ZN-2081...
> Linking HIS-119 ND1-952 and ZWA-262 ZN-2081...
>
> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
> Checking for duplicate atoms....
> ...
>
> But I get the following errors after grommp. grompp doesnt still throw
> errors. I think there is something weird about specbond.dat and
> ffbonded.itp?
>
> After grompp command:
> ERROR 1 [file protein.top, line 21983]:
>   No default Angle types

grompp is telling you to look at this line (and others). What is on it?
Which atom triple has no parameter definition grompp can find?

Mark