[gmx-users] Missing Interactions in [ angles ] Section in Topology

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 9 14:29:36 CET 2012 


Lara Bunte wrote:
> Hi
> 
> Thanks for the answer. For me I don't know where the problem is. 
> 
> 
>> The .rtp file would be necessary to understand what is expected in 
> the topology, as it is not clear to me why some lines have >explicit 
> parameters while others do not.
> 
> 
> I put my .rtp file in the appendix. Could you please take a look on it?
> 

What's happening here is that the angles explicitly listed in the .rtp file are 
shown in your .top, but there are other angles present for which you have not 
specified parameters.  These are the lines that have no explicit equilibrium 
angle and force constant.  They will be looked up in ffbonded.itp.

-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: 21:04 Mittwoch, 7.März 2012
> Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
> 
> 
> 
> Peter C. Lai wrote:
>> [ angles ] is defined in ffbonded.itp. If you have new angles you will
>> need to specify them there. grompp will read ffbonded.itp and try to correlate 
> 
> To be clear - [angles] can be specified in an .rtp file (but are not required, because pdb2gmx will by default generate all angles).  An [angletypes] directive in ffbonded.itp supplies the parameters for angles.
> 
>> it with the atomnumbers in the top file generated by pdb2gmx. If you modified
>> your top file by hand to include interactions which are missing from ffbonded.itp then grompp will complain about missing interactions (at least
>> that is my experience).
>>
> 
> Correct, but it is still not clear to me what the problem is here, if there is one.  The .rtp file would be necessary to understand what is expected in the topology, as it is not clear to me why some lines have explicit parameters while others do not.
> 
> -Justin
> 
>> On 2012-03-07 05:19:19PM +0000, Lara Bunte wrote:
>>> Hi Justin
>>>
>>>
>>> I am using a CHARMM27 force field. I create a pdb file with the coordinates of my molecule and I create a .rtp and a .hdb file for this. I also edit atomtypes.atp, ffnonbonded.itp and residuetypes.dat
>>>
>>> The parameters for the parametrization are out of a supporting information of a paper that did MD with my molecule. 
>>> The System is my molecule (isoalloxazine) in water. 
>>> Do you want to see my .rtp file?
>>>
>>> Thanks you 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: 20:34 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
>>>
>>> ========================================
>>> -- gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> -- gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> -- ========================================
> 
> 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
> 
> ========================================
> -- gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

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

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

More information about the gromacs.org_gmx-users mailing list