You said "You do not have to make changes in pdb file". Then How will I create .rtp file.
29 Aralık 2010 19:32 tarihinde Justin A. Lemkul <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>> 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>>> 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 >> >> >> >> Thanks in advance >> >> -- Ahmet YILDIRIM >> >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto: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> >> <mailto: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 <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
-- 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
