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

[Ahmet yıldırım]

Hi,

I modified ffbonded.itp. Eventually it works. Thanks Justin.
Now, there is another problem. System doesnt reach to converge in energy
minimization step.
After mdrun:
Steepest Descents converged to machine precision in 83 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -7.2871531e+05
Maximum force     =  1.4660705e+05 on atom 23980
Norm of force     =  1.9970358e+03

P.S.I simulated this structure before and I havent had any problems. I am
using that input/mdp files again.




2014-04-05 23:03 GMT+03:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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
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-- 
Ahmet Yıldırım