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.abra...@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.abra...@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@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-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
