[gmx-users] Re: Adding New Residue to the Gromos 53.6 ff
James Starlight
jmsstarlight at gmail.com
Mon Aug 6 10:00:58 CEST 2012
Mark,
The main difficulties is that ATB's output is in the form like
[ bonds ]
1 2 2 0.1000 1.8700e+07
1 3 2 0.1000 1.8700e+07
[ angles ]
; ai aj ak funct angle fc
2 1 3 2 109.50 380.00
2 1 4 2 109.50 425.00
3 1 4 2 109.50 425.00
[ dihedrals ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
7 8 10 9 2 0.00 167.36
8 10 9 11 2 0.00 167.36
10 9 11 7 2 0.00 167.36
etc
here I must replace the number of atoms by the corresponded real atoms
but also replace the values for the bonds, angles and dihedrals by the
Gromacs type codes ( e.g gb_1 etc). This is very routinely for me yet
:)
I've sent the letter to the ATB's developments with the same
proposition to five RTP as the output which could be in some cases
more usefull that ITP.
James
2012/8/5, Mark Abraham <Mark.Abraham at anu.edu.au>:
> 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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