[gmx-users] Re: Adding New Residue to the Gromos 53.6 ff

[Mark Abraham]

On 6/08/2012 4:11 PM, James Starlight wrote:
> Mark,
>
>
> I suppose that the most trivial way to include such external
> topologies is the placement of the ITP file at the bottom of the
> topol.top file ( and addition of two covalent bonds with the adjcent
> residues in case of GFP chromophore ) like in any potein-ligan system.

No, because bonded interactions can only occur within a [moleculetype].

> I think that it must be some script foe convertion itp ro rtp because
> both of that formats have a lot of differenties so the manually
> editing in case of big HET group is very routinely.

For the ~25 atoms of the GFP chromophore, given a reliable .itp of 
Ace-Gly-Cro-Gly-Nme or something, producing an .rtp entry by hand is a 
job of up to half an hour, if you understand the .rtp format. 
Particularly if the bonded interactions are from the main forcefield, 
you've only got to describe atom types, connectivity and charge.

You could make a feature request of the ATB people for .rtp output 
(which might come with supplemental forcefield .itp files).

Mark

>
> James
>
> 2012/8/5, Mark Abraham <Mark.Abraham at anu.edu.au>:
>> On 6/08/2012 4:31 AM, James Starlight wrote:
>>> Mark,
>>>
>>> 1) The error was because I've used topology of the CRO generated by
>>> the ATB in the ITP form in the RTP file.
>> No, the error "Residue 'CRO' not found in residue topology database"
>> means you haven't put it in the right place, but until you inspect your
>> pdb2gmx output for clues about where it is looking, to help find where
>> you haven't followed the right procedure, you're stuck. You've not told
>> us your command line or shown us any significant output, so you really
>> can't be helped.
>>
>>> E.g in RTP file I've found that [ atoms ] is simple
>>> C     C   0.450     1
>>>
>>> when in my ITP its more complicated
>>> 7     C    1    CRO     C1    5    0.089  12.0110
>>>
>>> the main difference is that RTP havent atom order where in IPT file
>>> the order of each group is specified.
>>> Is there any way to convert ITP back to RTP form ?
>> No. You'll have to do it by hand.
>>
>>> 2) I've used specbond.dat to define covalent bonds between C and N
>>> termi of chromophore and corresponded termi of the djacent residues (
>>> in GFP chromophore is covalently linked in the midle of the alph helix
>>> of that protein in both ends)
>> Sounds like a recipe for trouble, unless you know how to build a
>> two-chain peptide with correct termini into the same [moleculetype], and
>> get specbond.dat to work at the same time. It's possible, but why not
>> use the built in mechanism for head-to-tail peptide linking?
>>
>> Mark
>>
>>> James
>>>
>>> 2012/8/5, Mark Abraham <Mark.Abraham at anu.edu.au>:
>>>> James Starlight wrote
>>>>> Dear Gromac's users!
>>>>>
>>>>> I'm working with the GFP protein which has chromophore (CRO) group
>>>>> which is covalently bonded to the protein. I want to add new residue
>>>>> to the Gromos 53.6 ff. by means of algorithm described here.
>>>>>
>>>>>
>>>>> For that I've coppied files to my local work dirr and modify all of
>>>>> them in accordance to the above tutorial- I've coppied .itp of CRO to
>>>>> the aminoacids.rtp
>>>>>
>>>>> [ CRO ]
>>>>> [ atoms ]
>>>>> etc
>>>>>
>>>>> I've defined bonds of the djacent real amino acids in the specbond.dat
>>>> Seems dangerous from my memory of GFP. You should probably be making a
>>>> single residue for the whole chromophore, in which case a model that
>>>> does
>>>> not need specbond.dat is possible.
>>>>
>>>>
>>>> James Starlight wrote
>>>>> Finally I've defined CRO (as the protein) in the residuetypes.dat
>>>>>
>>>>> When I've try use pdb2gmx I've obtain error
>>>>>
>>>>> Fatal error:
>>>>> Residue 'CRO' not found in residue topology database
>>>>>
>>>>>
>>>>> What I've done wrong?
>>>>>
>>>> If
>>>> http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
>>>> and its links don't help, you'll have to inspect carefully your output
>>>> from
>>>> pdb2gmx for clues.
>>>>
>>>> Mark
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> View this message in context:
>>>> http://gromacs.5086.n6.nabble.com/Adding-New-Residue-to-the-Gromos-53-6-ff-tp4999959p4999960.html
>>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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