Dear Justin, Firstly, Thanks for your help. You said "You're going from the end of chain B to the beginning of chain A, then back to B later on. Also realize that whatever "ABSG" or "BSG" is." How do you understand it? Where can I find such an important theoretical information?
Thanks in advance 29 Aralık 2010 20:07 tarihinde Justin A. Lemkul <jalem...@vt.edu> yazdı: > > > ahmet yıldırım wrote: > >> OK. if I do what sort change in pdb file, there is no need to create .rtp >> file. It seems difficult to create the .rtp file. >> >> > That depends on whether you need this residue, hence all of my previous > questions. If there is some functional significance to this residue and you > need it for a simulation, then you'll either need to deal with the .rtp > file, which actually is not terribly difficult, it just involves a little > bit of reading and studying existing examples. Otherwise, if the molecule > is non-covalently bound to the protein, follow the tutorial I linked before, > and pay attention to the hint I gave you before about using PRODRG, which I > will reiterate more explicitly: the output topology from PRODRG will require > manual modification and validation. > > http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips > > -Justin > > Thanks for your help >> >> 29 Aralık 2010 19:49 tarihinde Justin A. Lemkul <jalem...@vt.edu <mailto: >> jalem...@vt.edu>> yazdı: >> >> >> >> >> ahmet yıldırım wrote: >> >> You said "You do not have to make changes in pdb file". >> >> >> When did I say that? >> >> >> Then How will I create .rtp file. >> >> >> That depends entirely upon what that residue is. Is it a >> constituent residue of the protein, such that its backbone is >> incorporated in the protein structure? Is it connected via a >> sidechain? Or is it a ligand? Any or all of the following might >> apply: >> >> http://www.gromacs.org/Documentation/File_Formats/.rtp_File >> >> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field >> http://www.gromacs.org/Documentation/File_Formats/specbond.dat >> http://www.gromacs.org/Documentation/Tutorials#General (Drug-enzyme >> complex, although beware the use of PRODRG) >> >> And, of course, the manual, which describes the contents of the .rtp >> file more thoroughly. >> >> -Justin >> >> 29 Aralık 2010 19:32 tarihinde Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >> <mailto:jalem...@vt.edu>>> yazdı: >> >> >> >> >> ahmet yıldırım wrote: >> >> Dear Justin, >> >> Thanks for your reply. Where is the error? >> >> Pdb file: >> >> ATOM 1 N ALA A 4 >> ATOM 2 CA ALA A 4 >> .... >> ATOM 2688 N ALA B 4 >> ATOM 2689 CA ALA B 4 >> .... >> ATOM 5449 OXT GLN B 361 >> TER 5450 GLN B 361 >> >> >> Right here. You're going from the end of chain B to the >> beginning >> of chain A, then back to B later on. Also realize that whatever >> "ABSG" or "BSG" is, it won't be recognized by pdb2gmx unless >> you've >> built a proper .rtp entry for it. >> >> -Justin >> >> HETATM 5451 OAAABSG A 1 >> HETATM 5452 OABABSG A 1 >> .... >> HETATM 5474 OAAABSG B 2 >> HETATM 5475 OABABSG B 2 >> .... >> HETATM 5492 O HOH A 2 >> HETATM 5493 O HOH A 362 >> HETATM 5494 O HOH A 363 >> .... >> HETATM 5744 O HOH B 362 >> HETATM 5745 O HOH B 363 >> >> 29 Aralık 2010 19:12 tarihinde Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> yazdı: >> >> >> >> >> >> ahmet yıldırım wrote: >> >> Dear Mark, >> >> The chain identifier have continuous. In sequence >> does >> not show >> any problem. >> >> >> >> Then you're not looking at the right contents; pdb2gmx >> wouldn't >> complain otherwise. Usually HETATM entries like HOH >> (water) are >> after all protein chains, so you might have chains A, >> B, C, >> etc for >> protein followed by A, B, C, etc for water. Have a >> more thorough >> look through the .pdb file. >> >> -Justin >> >> >> 29 Aralık 2010 15:10 tarihinde Mark Abraham >> <mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au>> >> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au>>> >> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au> >> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au>> >> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au> >> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au>>>>> yazdı: >> >> >> On 29/12/2010 10:12 PM, ahmet yıldırım wrote: >> >> Dear users, >> >> a...@ubuntu:~/Desktop/3O87$ pdb2gmx -f 3O87.pdb >> -water tip3p >> >> Select the Force Field: >> 5: OPLS-AA/L all-atom force field (2001 >> aminoacid >> dihedrals) >> >> Fatal error: >> Chain identifier 'A' was used in two >> non-sequential blocks >> (residue 710, atom 54 49) >> >> What should I do to correct this error? >> >> >> Look at the entries whose chain identifier is >> A, and >> see why they >> are non-sequential, and take suitable action to >> remedy. You >> may need >> to Google for the PDB file format if you don't >> already >> understand it. >> >> Mark >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@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-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Ahmet YILDIRIM >> > > -- > ======================================== > > 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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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