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

[James Starlight]

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.

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.

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.
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Only plain text messages are allowed!
>>> * 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
> * Only plain text messages are allowed!
> * 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
>