[gmx-users] Missing Interactions in [ angles ] Section in Topology
Lara Bunte
lara.bunte at yahoo.de
Mon May 14 23:15:29 CEST 2012
Hi
All needed parameters for [ angles ] in the topology are defined in my .rtp file parametrization and also in the ffbonded.itp in the CHARMM27 folder. This still don't work. In the topology my [ angles ] block looks like
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 19 1
1 2 3 1 123.75 250.00
1 2 4 1 117.47 230.00
3 2 4 1
2 4 5 1 115.95 105.00
So there are lines missing.
In my ffbonded.itp angles are all defined like
[ angletypes ]
; i j k func th0 cth ub0 cub
; f5: Urey-Bradley
NN3A CN1A ON1 5 123.75 250.00
NN3A CN1A NN2U 5 117.47 230.00
CN1A NN2U HN2 5 115.95 105.00
And in my .rtp file it looks like
; Col 1: angle classification
; Col 2: equilibrium bond angles in degrees
; COl 3: force constant in kcal/(mol*rad^2)
[ angles ]
N1 C2 O2 123.75 250.00
N1 C2 N3 117.47 230.00
C2 N3 H3 115.95 105.00
What is the problem? Why are there still this missing lines in the topology?
Thanks for helping me
Greetings
Lara
----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
CC:
Gesendet: 20:59 Montag, 7.Mai 2012
Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
On 5/7/12 2:54 PM, Lara Bunte wrote:
> Hi
>
> So you think that I should edit something in ffbonded.itp? The parameters that I would write by hand in the topology should be supplemented in the ffbonded.itp?
>
> I don't really know what I have to do concretely, to fix this problem.
>
>
If the parameters are not already present in the force field, you have 2 options:
1. Add them to ffbonded.itp - useful if you have multiple molecules that you
need to simulate
2. Add them to the topology - the easiest approach
Both effectively accomplish the same thing, but approach #2 is slightly more
straightforward and does not potentially affect all your simulations should
something go wrong.
-Justin
> Greetings
>
> Lara
>
>
>
>
>
> ----- Ursprüngliche Message -----
> Von: Justin A. Lemkul<jalemkul at vt.edu>
> An: Discussion list for GROMACS users<gmx-users at gromacs.org>
> CC:
> Gesendet: 21:59 Sonntag, 6.Mai 2012
> Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
>
>
>
> On 5/6/12 3:45 PM, Lara Bunte wrote:
>> Hi
>>
>> You said:
>>
>>> The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp.
>> I let the lines empty and I got an error at the first grompp, before energy minimization. grompp missed this empty lines. Here a part out of the errors:
>>
>> ERROR 28 [file topol.top, line 229]:
>> No default Angle types
>>
>>
>> ERROR 29 [file topol.top, line 233]:
>> No default Improper Dih. types
>>
>> My system is a cofactor, the force field is CHARMM27, parametrized with data out of a supporting information of a group that determined this parameters for my cofactor by experiments and quantum mechanical calculations. In residuetypes.dat I defined ISO Isoalloxazin. In the force field order I gave all informations (I guess).
>>
>> What could be the problem?
>>
>> I am able to complete the topol.top file by hand, but I really like to know what is the problem here.
>>
>
> A sequence of atoms in a topology (defined by atom type, not name or number) is
> mapped back to parameters in ffbonded.itp. If no suitable parameters are found,
> you get the error messages. In a normal topology (.top or .itp) for most force
> fields, the parameters are not explicitly stated because they are looked up in
> this manner. If you're introducing something new or overriding existing force
> field parameters, you need to explicitly include them in the topology or add
> them to the appropriate directive in ffbonded.itp.
>
> -Justin
>
>>
>> Thanks for help
>>
>> Greetings
>> Lara
>>
>>
>>
>>
>>
>> ----- Ursprüngliche Message -----
>> Von: Justin A. Lemkul<jalemkul at vt.edu>
>> An: Discussion list for GROMACS users<gmx-users at gromacs.org>
>> CC:
>> Gesendet: 20:34 Dienstag, 6.März 2012
>> Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
>>
>>
>>
>> Lara Bunte wrote:
>>> Hi
>>>
>>> In some lines the equilibrium angle and the force constant is missing.I give you an example:
>>>
>>>
>>> The [ angles ] section is build like
>>>
>>> [ angles ]
>>> ; ai aj ak funct c0 c1 c2 c3
>>> 2 1 19 1 123.75 250.00
>>> 1 2 3 1 123.75 250.00
>>> 1 2 4 1 117.47 230.00
>>>
>>>
>>>
>>> And my pdb2gmx output is for example something like
>>>
>>> [ angles ]
>>> ; ai aj ak funct c0 c1 c2 c3
>>> 2 1 19 1 123.75 250.00
>>> 1 2 3 1
>>> 1 2 4 1 117.47 230.00
>>>
>>>
>>
>> So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology?
>>
>> What force field are you using? What is the system? For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so "missing" parameters are completely normal and not problematic. If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes.
>>
>> In principle, there's nothing wrong with any of this. The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp. These parameters are only overwritten if explicitly present in the topology. If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error.
>>
>> -Justin
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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