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.
Thanks for your help 29 Aralık 2010 19:49 tarihinde Justin A. Lemkul <[email protected]> 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 <[email protected] <mailto: >> [email protected]>> 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 <[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> >> <mailto:[email protected]>>> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>> 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 | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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