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

[Justin Lemkul]

On 4/5/14, 10:38 PM, Ahmet yıldırım wrote:
> 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.
>

Presumably the previous runs were done with a different parameter set, so either 
(1) the .mdp files are inappropriate, (2) the applied force field parameters are 
incorrect in some way, or (3) the supplied geometry is somehow broken.  Given 
that mdrun is telling you where the problem is, visualization is your first step 
to figuring out what's going on.

-Justin

>
>
>
> 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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>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================